Tag: SAMtools

How to parallelize bcftools mpileup with GNU parallel?

I think that this would be a solution: I started with a file that contains the scaffold name and lengths: JH739887 30495534 JH739888 29527584 JH739889 22321128 […] I then added a column with “1” in it to make it the “start” position. Since the scaffolds are not placed on the…

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A bash question

A bash question 0 Hi, I have a set of human exome data sequenced with Agilent Sureselect XT HS2. I am following the Best practice document www.agilent.com/cs/library/software/public/AGeNTBestPractices.pdf On p.3 the example for bwa, just want to check if this is correct before starting the long process for alignment. especially the…

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Circos plot of WGS assembly

Hello singh.bioinfo, I was able to generate a comparative Circos plot of two plant genome assemblies by using someone else’s code and some manual edits of the configuration files. The first step is to ensure that the two assemblies have different chromosome/contig/scaffold IDs in the fasta file. The second is…

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Samtools mpileup – I’m getting different number of base calls compared to number of quality scores

Edit: Summary: In the mpileup file, I have different number of quality scores than base calls. For example, I might have 342 reads covering a position, but there will be 340 base calls. This makes parsing the mpileup file difficult Edit: I should note that the mpileup I’m using was…

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failed to write header to “-“

[bam_sort_core] merging from 32 files and 16 in-memory blocks… samtools sort: failed to write header to “-“ 0 Hi, When I run script samtools sort -@ 16 -T “path/to/temp” “$bamfile” > “$_sorted.bam, I get this error message: [bam_sort_core] merging from 112 files and 16 in-memory blocks… samtools sort: failed to…

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[ERROR] dual gap penalties violating E1>E2 and O1+E1

Minimap2 error: [ERROR] dual gap penalties violating E1>E2 and O1+E1<O2+E2 0 Hi, I’m trying to run minimap2 to assemble Oxford Nanopore reads to a reference but I keep getting the following error: [ERROR] dual gap penalties violating E1>E2 and O1+E1<O2+E2. Here is the command I’m running: minimap2 -s 10 -t…

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Index genome not working in Tracy

I’m trying to follow the variant calling guide for Tracy. www.gear-genomics.com/docs/tracy/cli/#variant-calling I have a viral genome just as a fasta file, and when I try to call variants like this: tracy decompose -v -a cmv -r CMVrefGenome.fasta -o oututfile inputfile.ab1 It tells me the genome needs to be shorter than…

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SQTagUtil – htsjdk 1.134 javadoc

Latest version of com.github.samtools:htsjdk javadoc.io/doc/com.github.samtools/htsjdk Current version 1.134 javadoc.io/doc/com.github.samtools/htsjdk/1.134 package-list path (used for javadoc generation -link option) javadoc.io/doc/com.github.samtools/htsjdk/1.134/package-list Read more here: Source link

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Lead Data Scientist – Bioinformatics job with Spark Therapeutics

Primary Duties The Bioinformatics Group within the Data Science Organization at Spark Therapeutics is seeking an engaged and passionate Lead Data Scientist with a focus on bioinformatics and computational biology to participate in and support projects involving omics and other high-dimensional data across the Technology & Research Organizations. He/she will…

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Visualiation of samtools depth output in a plot

Visualiation of samtools depth output in a plot 1 Hei everyone, for my project i did capture sequencing of mulitple individuums. Somehow the depth and coverage is not as high as expected. Now i want to plot the output of samtools depth. Unfortunatly i am not able to write a…

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filtering out nanopore reads by alignment score

filtering out nanopore reads by alignment score 1 I am trying to filter out mitochondrial-specific nanopore reads from whole genome reads using minimap2 and samtools view. In addition I want to retain reads with an alignment score of 5000 or more, following a methodology suggested on a paper. However I…

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The Biostar Herald for Tuesday, October 26, 2021

The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from GenoMax, Istvan Albert, lethalfang, and was edited…

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DESeq2 input file

DESeq2 input file 1 Hello. I’m trying to analyzing RNA-seq data with DESeq2 to study differencial gene expression. I have SAM and BAM files generated by samtools. How do I insert my files on R to run DESeq2? Do I use the SAM files, BAM files or sorted BAM files?…

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Greatly speed up conda by using mamba

Conda has been my go-to software manager, but it was only recently brought to my attention that a well maintained project has aimed to greatly speed up and improve the conda functions. Mamba is an almost complete rewrite of conda in C++, allows for parallel downloading of data, and has…

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format not a string literal and no format arguments [-Werror=format-security]

Processing control commands: > tags -1 confirmed fixed-upstream pending Bug #997180 [src:samtools] samtools: FTBFS: bam_tview_curses.c:88:5: error: format not a string literal and no format arguments [-Werror=format-security] Added tag(s) pending, confirmed, and fixed-upstream. > forwarded -1 github.com/samtools/samtools/pull/1509 Bug #997180 [src:samtools] samtools: FTBFS: bam_tview_curses.c:88:5: error: format not a string literal and no…

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read depth using samtools

read depth using samtools 1 Hello all, I’m using samtools in order to get the depth of a file called file.bam, but the output I have is like this: samtools depth file.bam > output.txt 11 88911833 2 11 88911834 2 11 88911835 2 I understand that the first column is…

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AbstractReader – htsjdk 1.140 javadoc

Latest version of com.github.samtools:htsjdk javadoc.io/doc/com.github.samtools/htsjdk Current version 1.140 javadoc.io/doc/com.github.samtools/htsjdk/1.140 package-list path (used for javadoc generation -link option) javadoc.io/doc/com.github.samtools/htsjdk/1.140/package-list Read more here: Source link

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marked as pending in samtools

Control: tag -1 pending Hello, Bug #997180 in samtools reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: salsa.debian.org/med-team/samtools/-/commit/488881b3a4b634343d9626646d0f00b469834a91 ———————————————————————— Add fix-ftbfs-mvprintw.patch Closes: #997180 ———————————————————————— (this message…

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Low assigned alignments

Low assigned alignments 0 Basecalls performed using CASAVA version v1.8.2 Trimmed reads with fastx_quality_trimmer 0.0.13 with a quality treshhold of 18 and a length of 20 Aligned with Bowtie 2.1.0 and Tophat 2.0.10 using Gencode v19 junctions Samtools 0.1.19-44428cd to make a bam, sort, index Raw counts were generated using…

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Discrepancy between samtools bedcov and pysam.count

I’m writing a new version of a tool and I’m trying to implement some functionality using pysam that was previously implemented using samtools bedcov. For example, here is a sample output of samtools bedcov test.bed tcga_test.bam -Q 50: chr19 50858094 50858095 64004 chr19 50858128 50858129 63170 chr19 50858162 50858163 51889…

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Bioinformatics Scientist with Security Clearance job in Bethesda at Dawson

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Paired-end reads somehow counted twice?

Paired-end reads somehow counted twice? 0 Hi. I’m new in Bioinformatics and try to extract read counts from fastq files. I compared my result with answer count matrix, and read counts are doubled. (Left one is from the answer read count matrix, and right one is my result.) I used…

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Numerical result out of range

samtools: Numerical result out of range 1 I am working with a SAM file (created with hisat2) with header: @SQ SN:chr1A LN:594006513 @SQ SN:chr1B LN:693261537 … When doing sorting and indexing, I get this error with samtools: [E::hts_idx_check_range] Region 536907741..536907892 cannot be stored in a bai index. Try using a…

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Does bcftools call ignore duplicate markings?

Does bcftools call ignore duplicate markings? 0 I am using Picard MarkDuplicates to mark duplicates in my position sorted BAM. Then, I variant call using bcftools mpileup and bcftools call like so: bcftools mpileup -f reference.fa positionsort.bam | bcftools call -mv -Ob -o calls.bcf To my knowledge, bcftools mpileup ignores…

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Oxford Nanopore Variant Calling Pipeline Calls Very Few of Variants of NA12878

Hello everyone, First, I am so sorry for this long and very amateur question. I am trying to build a pipeline for SNP calling for Oxford Nanopore MinION based long reads. I need to test the pipeline but apparently the number of test data is really low. I only have…

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Loop for merging multiple BAM files from multiple lanes with different names into related names/ samstat

Loop for merging multiple BAM files from multiple lanes with different names into related names/ samstat 0 Hi all, I’m a beginner in analysis and don’t have any help to check my codes or ask for solutions so I’ll post my questions here. I have a chip seq data and…

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HsMetricCollector (gatk 4.0.5.0 API)

HsMetricCollector (gatk 4.0.5.0 API) JavaScript is disabled on your browser. public class HsMetricCollector extends TargetMetricsCollector<HsMetrics> Calculates HS metrics for a given SAM or BAM file. Requires the input of a list of target intervals and a list of bait intervals. Can be invoked either on an entire iterator of SAMRecords…

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Bristol Myers Squibb hiring Senior Scientist, Translational Bioinformatics in Princeton, New Jersey, United States

At Bristol Myers Squibb, we are inspired by a single vision – transforming patients’ lives through science. In oncology, hematology, immunology and cardiovascular disease – and one of the most diverse and promising pipelines in the industry – each of our passionate colleagues contribute to innovations that drive meaningful change….

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FASTQ to VCF pipeline question

FASTQ to VCF pipeline question 0 Hello all, I am new with programming within bioinformatics and long story short, I’m practicing writing pipeline scripts starting with the fastq to VCF pipeline. I am basically at the point where I went from fastq to sorted-bam files, and as I went to…

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Error due to Sam to Bam and Indexing using picard

Error due to Sam to Bam and Indexing using picard 0 Hii all, I ran the following command: picard SortSam -I 10100123749_NIKEC.bam -O 10100123749.bam –SORT_ORDER coordinate –MAX_RECORDS_IN_RAM 1500000 –VALIDATION_STRINGENCY LENIENT But I am getting this error: 18:09:18.048 INFO NativeLibraryLoader – Loading libgkl_compression.so from jar:file:/home/mdrcubuntu/anaconda3/envs/smruti/share/picard-2.26.3-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so [Mon Oct 18 18:09:18 IST 2021]…

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FeatureReader – htsjdk 1.133 javadoc

Latest version of com.github.samtools:htsjdk javadoc.io/doc/com.github.samtools/htsjdk Current version 1.133 javadoc.io/doc/com.github.samtools/htsjdk/1.133 package-list path (used for javadoc generation -link option) javadoc.io/doc/com.github.samtools/htsjdk/1.133/package-list Read more here: Source link

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BamIndexValidator.IndexValidationStringency – htsjdk 2.2.2 javadoc

Latest version of com.github.samtools:htsjdk javadoc.io/doc/com.github.samtools/htsjdk Current version 2.2.2 javadoc.io/doc/com.github.samtools/htsjdk/2.2.2 package-list path (used for javadoc generation -link option) javadoc.io/doc/com.github.samtools/htsjdk/2.2.2/package-list Read more here: Source link

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MethylDackel Error running on HPC server

Hello, I am trying to analyze data for RRBS (reduced representation bisulfite sequencing) and want to use BWA-METH for alignment. I also ran Bismark, but bismark output only shows mapping efficiency of 33.8% while BWA-METH shows 99.8% mapping efficiency (paired-end). So, I converted .sam to .bam with samtools and tried…

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LTF8 – htsjdk 2.0.1 javadoc

Latest version of com.github.samtools:htsjdk javadoc.io/doc/com.github.samtools/htsjdk Current version 2.0.1 javadoc.io/doc/com.github.samtools/htsjdk/2.0.1 package-list path (used for javadoc generation -link option) javadoc.io/doc/com.github.samtools/htsjdk/2.0.1/package-list Read more here: Source link

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Output file from samtools index is empty

Output file from samtools index is empty 0 Hello, I haven’t been able to find anything related to this question. For some strange reason after indexing .BAM file the output .BAI file is empty. No error message is shown, neither the output itself is empty (the file is created after…

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Count number of unique alignments to each chromosome from sam file

Count number of unique alignments to each chromosome from sam file 0 Hi, I want to count the number of unique reads aligned to each chromosome after mapping to the genome. I don’t mind if something is multimapped, say if read A maps to both chr3 and chr6 that is…

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Feat/support passing index files – githubmemory

v1.10 brought about the new -X option (-X include customized index file), to samtools. github.com/samtools/samtools/pull/978 Is it possible to request for tabix/bcftools/etc? Use case would be for passing in signed s3 urls into all of the various tools. e.g. tabix <signed_vcf_url> -X <signed_vcf_tbi_url> chr2 bcftools view <signed_vcf_url> -X <signed_vcf_tbi_url> chr2…

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paired reads have different names BWA MEM after samtools bam > fastq

paired reads have different names BWA MEM after samtools bam > fastq 0 I have used bwa mem to align to a host genome and output the unmapped reads. I have then sorted this resulting BAM and split into pairs fastq files. Whya fter sorting the BAM file am I…

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mapping long-reads to a reference library

mapping long-reads to a reference library 1 Hi, I have long, pacbio, reads and I have a reference library of only repeats, I want to map the long reads on the repeats library using bwa mem, is this command correct? bwa index mmm.pacbio.fastq.gz bwa mem mmm.pacbio.fastq.gz repeat-library.fasta | samtools sort…

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SortingCollection.Codec – htsjdk 1.139 javadoc

Latest version of com.github.samtools:htsjdk javadoc.io/doc/com.github.samtools/htsjdk Current version 1.139 javadoc.io/doc/com.github.samtools/htsjdk/1.139 package-list path (used for javadoc generation -link option) javadoc.io/doc/com.github.samtools/htsjdk/1.139/package-list Read more here: Source link

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How do I compare reads between two bam file?

How do I compare reads between two bam file? 1 I would like to find reads in one bam files which are not in a second bam file. Is there an easy way to do this? My way for now is: sort both bam files by read name extract read…

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Splitted sorted BAM files with samtools

Splitted sorted BAM files with samtools 1 Hello. I’m trying to use the command “sort” of samtools (ex: samtools sort alignment.bam -o alignment.sorted.bam), but for some reason, instead of generating one single sorted file (ex: alignment.sorted.bam) it generates many files (ex: alignment.sorted.bam.0000.bam, alignment.sorted.bam.0001.bam, alignment.sorted.bam.0002.bam, …, alignment.sorted.bam.0020.bam). The odd thing is…

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SAMtools markdup and insert size in Qualimap

I am using Qualimap to do some Quality Control (QC) of my bowtie2 alignment and also to compare QC reports when I mark duplicates in the BAM file using samtools markdup. While comparing these reports, I noticed a difference in the insert sizes that Qualimap gives. For example: One of…

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SamReader.Indexing – htsjdk 2.1.1 javadoc

Latest version of com.github.samtools:htsjdk javadoc.io/doc/com.github.samtools/htsjdk Current version 2.1.1 javadoc.io/doc/com.github.samtools/htsjdk/2.1.1 package-list path (used for javadoc generation -link option) javadoc.io/doc/com.github.samtools/htsjdk/2.1.1/package-list Read more here: Source link

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samtools to count the number of reads mapped to each spike-in for each sample

samtools to count the number of reads mapped to each spike-in for each sample 0 My goal is to use STAR to create a new genome with the spike-ins listed below by combining both hg38.fa and spike-in. Once I have the genomes created, I’ll align FASTQs to this newly created…

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Did not inflate expected amount error

SAMFormatException: Did not inflate expected amount error 0 I am facing an error while running GATK Basecalibrator. [1 July 2021 at 5:00:42 PM IST] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 35.00 minutes. Runtime.totalMemory()=791674880 htsjdk.samtools.SAMFormatException: Did not inflate expected amount at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:147) at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:96) at htsjdk.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:550) at htsjdk.samtools.util.BlockCompressedInputStream.processNextBlock(BlockCompressedInputStream.java:532) at htsjdk.samtools.util.BlockCompressedInputStream.nextBlock(BlockCompressedInputStream.java:468) at htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:458) at…

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SAM Validation Error with CleanSam (Aligment start must be

SAM Validation Error with CleanSam (Aligment start must be <= reference seq length) 0 I ran several bam files through a pipeline with CleanSam, SortSam, and MarkDuplicates without a problem. However, one of the input files gave me the following error with CleanSam: ERROR: Record 2106053, Read name A00187:414:HMYCYDSXY:3:1426:13367:11083, Alignment…

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The population genomic structure of green turtles (Chelonia mydas) suggests a warm-water corridor for tropical marine fauna between the Atlantic and Indian oceans during the last interglacial

Alfaro-Nunez A, Bertelsen MF, Bojesen AM, Rasmussen I, Zepeda-Mendoza L, Olsen MT et al. (2014) Global distribution of Chelonid fibropapilloma-associated herpesvirus among clinically healthy sea turtles. BMC Evol Biol 14:206 PubMed  PubMed Central  Article  Google Scholar  Ali OA, O’Rourke SM, Amish SJ, Meek MH, Luikart G, Jeffres C et al….

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Mapping MISeq reads to a single gene

Mapping MISeq reads to a single gene 0 Hello community, I am really new to genome analyses and i would like to use the community’s wisdom! I have two simple tasks. Map MiSeq reads and call SNPs on 1)DNA and 2)RNA. Let me elaborate: 1) I want to simply identify…

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samtool sort

samtool sort 0 my command :bowtie2 -x Guy11 -1 Guy11_FDSW210137750-1r_1.clean.fq.gz -2 Guy11_FDSW210137750-1r_2.clean.fq.gz | samtools sort -O bam -@ 5 -o Guy11.bam and then it got error sort: invalid option — ‘O’ open: No such file or directory [bam_sort_core] fail to open file bam Can people help me ? genomics analysis…

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How to assemble read with a minimum 2 coverage per site

How to assemble read with a minimum 2 coverage per site 0 Hi, I have a query regarding read assembly I have a bam file I made a consensus sequence but I want to make a consensus sequence with a minimum of 2 coverage per site instead of full coverage…

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Trouble installing HiC-Pro

Trouble installing HiC-Pro 0 Hello, I am trying to install HiC-Pro on a slurm cluster but I am getting errors. I downloaded the Hi-C Pro repository to my system and created the HiC-Pro_v3.1.0 environment from the environment.yml file. I then ran the commands “make configure” and “make install”. I updated…

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Twist Bioscience Staff Bioinformatics Engineer, Biopharma

Twist Biopharma is seeking a Bioinformatics Engineer to develop and integrate workflows, analyses, and computational tools involved in the production and research of antibodies and proteins. While you have a broad interest in biotech and related scientific technologies, you also understand that computer science resources must be utilized to reach…

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htsjdk.samtools.CSIIndex.getFirstLocusInBin java code examples | Tabnine

@Test public static void testGetFirstLocusInBin() { Assert.assertEquals(csi.getFirstLocusInBin(bin1), 1); Assert.assertEquals(csi.getFirstLocusInBin(bin2), 1); Assert.assertEquals(csi.getFirstLocusInBin(bin3), 1); Assert.assertEquals(csi.getFirstLocusInBin(bin4), 1); Assert.assertEquals(csi.getFirstLocusInBin(bin5), 1); Assert.assertEquals(csi.getFirstLocusInBin(bin6), (1<<17) + 1); Assert.assertEquals(csi.getFirstLocusInBin(bin7), (1<<20)*7 + 1); Assert.assertEquals(csi.getFirstLocusInBin(bin8), (1<<14)*8 + 1); Assert.assertEquals(ucsi.getFirstLocusInBin(bin1), 1); Assert.assertEquals(ucsi.getFirstLocusInBin(bin2), 1); Assert.assertEquals(ucsi.getFirstLocusInBin(bin3), 1); Assert.assertEquals(ucsi.getFirstLocusInBin(bin4), 1); Assert.assertEquals(ucsi.getFirstLocusInBin(bin5), 1); Assert.assertEquals(ucsi.getFirstLocusInBin(bin6), (1<<18) + 1); Assert.assertEquals(ucsi.getFirstLocusInBin(bin7), (1<<21)*7 + 1); Assert.assertEquals(ucsi.getFirstLocusInBin(bin8), (1<<15)*8 + 1);…

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kallisto genomebam not showing reads on igv

Hello! I am trying to produce bam files to load to igv after kallisto quant with –genobam option. After producing and loading the pseudoalignment bam to the igv, it is empty. This is my initial command: kallisto quant -i Homo_sapiens.GRCh38.cdna.all.release-100.idx -o pseudo -t 10 –genomebam -g Homo_sapiens.GRCh38.100.gtf -c hg38.chrom.sizes R1.fastq.gz.trim_1.fq.gz…

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command not found, in IMPUTE2

Edit June 7, 2020: The code below is for phased imputation using the output of SHAPEIT2 and ultimate production of phased VCFs. For the initial pre-phasing process with SHAPEIT2, see my answer here: Phasing with SHAPEIT So, the steps are usually: pre-phasing into pre-existing haplotypes available from HERE ( Phasing…

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Bioinformatics Scientist Job Opening in Huntsville, AL at Discovery Life Sciences

Discovery Life Sciences are the Biospecimen and Biomarker Specialists™ serving thousands of scientists across the U.S. and around the world. We’re looking for a standout Bioinforatics Scientist for the HudsonAlpha Discovery sequencing lab in Huntsville, Alabama. The Bioinformatics Scientist contributes to our mission by taking lab-generated data and creating computational…

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The genome of Shorea leprosula (Dipterocarpaceae) highlights the ecological relevance of drought in aseasonal tropical rainforests

Sequencing of Shorea leprosula genome Sample collection Leaf samples of S. leprosula were obtained from a reproductively mature (diameter at breast height, 50 cm) diploid tree B1_19 (DNA ID 214) grown in the Dipterocarp Arboretum, Forest Research Institute Malaysia (FRIM). DNA extraction Genomic DNA was extracted from leaf samples using the…

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Index of /examples/archive/bioinfo/samtools

Index of /examples/archive/bioinfo/samtools Samtools/BCFtools/HTSlib Introduction and Notes Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories: Samtools Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format BCFtools Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants HTSlib A C library for reading/writing high-throughput sequencing data…

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Comparative cellular analysis of motor cortex in human, marmoset and mouse

Statistics and reproducibility For multiplex fluorescent in situ hybridization (FISH) and immunofluorescence staining experiments, each ISH probe combination was repeated with similar results on at least two separate individuals per species, and on at least two sections per individual. The experiments were not randomized and the investigators were not blinded…

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chimeric vs unaligned reads

Forum:chimeric vs unaligned reads 0 Hello, I’m trying to obtain the chemic alignments from a BAM file that originally was generated by STAR and that only has a list of unaligned reads at the end of the file (so no SA tag). If I convert that BAM file back into…

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conda stop to install or work

conda stop to install or work 1 Hi, I need help please I have Mac Bigsur conda suddenly stop working or installing or even uninstalling I believe that there’s an issue in the env. I’ve been tried many solutions but still the same ! conda install -c bioconda samtools Collecting…

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How To Extract A Sequence From A Big (6Gb) Multifasta File ?

How To Extract A Sequence From A Big (6Gb) Multifasta File ? 11 I want to extract some sequences using ID from a multifasta file. Using perl is not possible because it gave an error when indexing the database. Maybe because of it’s size? Is there any way to this…

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Convert VCF file to mpileup

Convert VCF file to mpileup 0 I am working on an iterative analysis that uses mpileup.txt files as input for a visualization step. This requires me to convert VCF files to mpileup.txt. There are plenty of examples for using samtools and bcftools to produce an intermediate mpileup file that is…

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Extracting exon level read coverage of a specific gene

HTSeq – Extracting exon level read coverage of a specific gene 1 Dear all, I am trying to quantify RNASeq reads at the “exon level” using HTSeq. To achieve a quantitative exon comparison. I am using ENCODE mouse data which is Illumina reads alligned to GENCODE M27 (GRCm39) using STAR…

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Very high read count variation in WGS alignments

Very high read count variation in WGS alignments 0 Hello everyone, I am new to NGS analysis, but have tried to learn through test data before starting with my own data. And now, it seems I am stuck somewhere. So, looking for some help/suggestions/ideas for the same. I have few…

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Identify Mapped reads and Unmaped Mate pairs

Identify Mapped reads and Unmaped Mate pairs 0 Hey, I have a sorted bam file which i got by mapping with reference. I want to identify two things from this bam file. How many reads mapped to each gene/contig in my bam file. As this was paired-end data, i want…

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0 + 0 mapped when used flagstat

0 + 0 mapped when used flagstat 1 I’ve downloaded bam files from ENA, and tried samtools flagstat to confirm mapping. But the result was like this. How do I interpret this? Should I download fastq files? Thanks mapping RNA-seq • 23 views You may have downloaded unaligned BAM (uBAM)…

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SamQL: a structured query language and filtering tool for the SAM/BAM file format | BMC Bioinformatics

Our primary aim building SamQL was flexibility and high expressivity for complex queries, similar to classic SQL. Table 1 compares the expressivity of SamQL for a relatively complex query against other widely used tools such as SAMtools, Sambamba, and naive Bash. SamQL maintains consistency on complex queries involving coordinates. However,…

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Using samtools to read a bam file

Using samtools to read a bam file 0 Hi all. I am trying to extract some information (please see below) from a bam file using samtools. Given my lack of experience, I am struggling. 1.) Total reads aligned on the forward strand 2.) Total reads aligned on the reverse strand…

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GenomicIndexUtil – htsjdk 1.143 javadoc

Latest version of com.github.samtools:htsjdk javadoc.io/doc/com.github.samtools/htsjdk Current version 1.143 javadoc.io/doc/com.github.samtools/htsjdk/1.143 package-list path (used for javadoc generation -link option) javadoc.io/doc/com.github.samtools/htsjdk/1.143/package-list Read more here: Source link

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Research Assistant in Genomics / Bioinformatics Jobs at Nutrition Technologies , Singapore

Less than a year of experience Important Information Make sure you’re applying to a legit company by checking their website and job posts. Job description Research Assistant in Genomics / Bioinformatics Nutrition Technologies Nutrition Technologies is an innovative company producing insects as a sustainable protein source for the animal feed…

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Accepted samtools-legacy 0.1.19+dfsg-4 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Fri, 01 Oct 2021 17:04:40 +0200 Source: samtools-legacy Architecture: source Version: 0.1.19+dfsg-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag…@lists.alioth.debian.org> Changed-By: Andreas Tille <ti…@debian.org> Changes: samtools-legacy (0.1.19+dfsg-4) unstable; urgency=medium . * Team upload. * Fix watchfile to detect new…

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Metaphlan Conda Repository – githubmemory

Hi @MichWeb75, the requirements you mentioned here is related to MetaPhlAn2, which had to use a specific version of samtools since StrainPhlAn was requiring a specific output format that was kept only to such versions. If you are not interested in using StrainPhlAn, you can upgrade samtools to a more…

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Subsampling Bam File With Samtools

Subsampling Bam File With Samtools 2 Hi, I am trying to subsample from a bam file using the samtools view -s command. This is working when sampling 50% or lower (-s 42.50, 42 being the seed), but anything higher fails (returns an empty file). He are the exact commands i…

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Unable to overcome troubles in whole exome analysis

Unable to overcome troubles in whole exome analysis 0 Hi, I am working on whole exome sequencing data whose pipeline has been standardized in the lab as such – Align with bwa-mem –> SortSam based on coordinates with Picard –> MarkDuplicates –> Remove sequencing duplicates –> Variant calling –> BQSR…

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biopython extract sequence from fasta

My two questions are: What is the simplest way to do this? This unique book shows you how to program with Python, using code examples taken directly from bioinformatics. using python-bloom-filter, just replace the set with seen = BloomFilter(max_elements=10000, error_rate=0.001). This book is suitable for use as a classroom textbook,…

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Plasmodium falciparum is evolving to escape malaria rapid diagnostic tests in Ethiopia

Study design and data collection We performed a cross-sectional, multisite study in 11 districts along Ethiopia’s borders with Eritrea, Sudan and South Sudan, located within three of its nine administrative regions. On average, ten health facilities were selected from each district, including four districts of Amhara Region (northwest Ethiopia), six…

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VGEA: an RNA viral assembly toolkit

This article was originally published here PeerJ. 2021 Sep 6;9:e12129. doi: 10.7717/peerj.12129. eCollection 2021. ABSTRACT Next generation sequencing (NGS)-based studies have vastly increased our understanding of viral diversity. Viral sequence data obtained from NGS experiments are a rich source of information, these data can be used to study their epidemiology,…

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Index of /kali/pool/main/s/samtools

Name Last modified Size Description Parent Directory   –   samtools-test_1.11-1_all.deb 2020-10-01 19:45 2.1M   samtools-test_1.13-2_all.deb 2021-08-30 19:13 2.1M   samtools_1.7-2+b1_amd64.deb 2018-05-05 16:29 400K   samtools_1.7-2+b1_arm64.deb 2018-05-05 14:56 371K   samtools_1.7-2+b1_armel.deb 2018-05-05 17:57 365K   samtools_1.7-2+b1_armhf.deb 2018-05-05 22:57 369K   samtools_1.7-2+b1_i386.deb 2018-05-05 17:41 418K   samtools_1.11-1.debian.tar.xz 2020-10-01 19:04 20K  …

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samtools view module output format and output file issues

output: tuple val(meta), path(“*.bam“), emit: bam path “*.version.txt“ , emit: version script: def software = getSoftwareName(task.process) def prefix = options.suffix ? “${meta.id}${options.suffix}“ : “${meta.id}“ “”” samtools view $options.args $bam > ${prefix}.bam There could be two issues with the current code in the samtools view module: samtools view $args input.bam >…

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Difference in .bed target region base count and mapped base count for different tools

Difference in .bed target region base count and mapped base count for different tools 1 Hello! I was initially doing performance comparison for tools to obtain sample wide average depth of coverage. I compared several tools listed below Qualimap, GATK – DepthOfCoverage, Mosdepth and Samtools – Bedcov However, the tools…

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Using HTSeq-count for paired-end data but unsorted by SAMTOOLS

Using HTSeq-count for paired-end data but unsorted by SAMTOOLS 1 Hi there, as per thread title. If I am using HTSeq-count on paired-end mapped BAM files, but they are unsorted, and I use -s yes on the default option, is it advisable? htseq ngs • 99 views Paired-end .bam need…

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Tools To Calculate Average Coverage For A Bam File?

Tools To Calculate Average Coverage For A Bam File? 12 I would like to get the average coverage of all the captured bases in a bam file. What would be the best way to do this? What I am looking is a simple one number like 40X. Given that there…

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No such file or directory

building bcftools: curl/curl.h: No such file or directory 2 I use to putty git clone –recurse-submodules git clone cd bcftools make <-The following error occurs in this area. hfile_libcurl.c:47:10: fatal error: curl/curl.h: No such file or directory 47 | #include <curl/curl.h> | ^~~~~~~~~~~~~ compilation terminated. make[1]: *** [Makefile:164:…

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bcftools

bcftools 0 I use to putty git clone –recurse-submodules git clone cd bcftools make <-The following error occurs in this area. hfile_libcurl.c:47:10: fatal error: curl/curl.h: No such file or directory 47 | #include <curl/curl.h> | ^~~~~ compilation terminated. make[1]: [Makefile:164: hfile_libcurl.o] Error 1 make[1]: Leaving directory ‘/home/kang/project/htslib’ make: [../htslib/htslib.mk:159: ../htslib/hts-object-files]…

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Mapping multiples

Mapping multiples 1 Hi, I am coming to you for help. I am doing a mapping on short and long read files with BWA and MINIMAP2 My problem is that, I want to make an if loop that would allow me to choose either BWA if I work with short…

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Problem with viewing BAM files in IGV

Problem with viewing BAM files in IGV 1 Hi everyone, I’m quite new to bioinformatics and I’m having some beginner problems with IGV. I’ve got some BAM files that were generated using the GATK best practice pipeline for SNP discovery, with BAI files located in the same directory. I’m using…

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Trouble running vcf2bam jvarkit tool

Trouble running vcf2bam jvarkit tool 2 I am trying to use the tool called vcf2bam from jvarkit on a server and I have the following 2 files: GRCh38_latest_genomic.fna – the file is of format FASTQ , and 00-common_all.vcf. I used samtools faidx and also picard CreateSequenceDictionary, but when I try…

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Single-cell DNA and RNA sequencing reveals the dynamics of intra-tumor heterogeneity in a colorectal cancer model | BMC Biology

Organoid culture of small intestinal cells and lentiviral transduction C57BL/6J mice and BALB/cAnu/nu immune-deficient nude mice were purchased from CLEA Japan (Tokyo, Japan). The small intestine was harvested from wild-type male C57BL/6J mice at 3–5 weeks of age (Additional file 1: Figure S9A). Crypts were purified and dissociated into single cells,…

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Why are my Nextflow processes not executing in parallel?

I have written a Nextflow script with three process: The first process takes a pair of fastq files and aligns with reference genome. The process writes the resulting SAM file into sam channel. Second process takes input from the sam channel and creates a BAM file from it, and writes…

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Count 5’End Mapped To A Specific Genomic Position

Count 5’End Mapped To A Specific Genomic Position 7 I got several SAM/BAM files, and I am interested in 5’ends of the mapped reads. Is there any tools or scripts to count how many 5’ends are mapped at a specific genomic position? N.B. I am not try to count the…

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Bedtools: Merging Many Bed Files

Bedtools: Merging Many Bed Files 2 I am using the algorithm CookHLA for my research. As part of its preparation, I need to feed it a bed file representing at least 100 of my samples. I have made the bed files for 500 samples using samtools and bedtools in a…

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Issues installing Pindel from git

Issues installing Pindel from git 1 I’m currently attempting to install Pindel on my ubuntu machine (16.04 server), but have been having issues with running the ./INSTALL file. The ./INSTALL file takes the path to htslib as an argument, so I also installed htslib from git with git clone github.com/samtools/htslib

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net.sf.samtools.SAMTextHeaderCodec$ParsedHeaderLine java code examples | Tabnine

private void parsePGLine(final ParsedHeaderLine parsedHeaderLine) { assert(HeaderRecordType.PG.equals(parsedHeaderLine.getHeaderRecordType())); if (!parsedHeaderLine.requireTag(SAMProgramRecord.PROGRAM_GROUP_ID_TAG)) { return; } final SAMProgramRecord programRecord = new SAMProgramRecord(parsedHeaderLine.removeValue(SAMProgramRecord.PROGRAM_GROUP_ID_TAG)); transferAttributes(programRecord, parsedHeaderLine.mKeyValuePairs); mFileHeader.addProgramRecord(programRecord); } Read more here: Source link

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cellranger count DETECT_COUNT_CHEMISTRY (failed)

cellranger count DETECT_COUNT_CHEMISTRY (failed) 0 I am learning scRNA-seq and the tutorial I follow uses dataset (1k pbmcs from healthy donor) from 10X genomics website. I downloaded fastq and reference transcriptome files and ran following command. cellranger-6.1.1/cellranger count –id pbmc_1k_v2_example –transcriptome /home/murat/Share/single_cell/refdata-gex-GRCh38-2020-A –fastqs /home/murat/Share/single_cell/pbmc_1k_v2_fastqs I get following message. Martian Runtime…

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How to pipe awk of bed file into samtools to extract fasta sequences?

How to pipe awk of bed file into samtools to extract fasta sequences? 1 I have a bed file (seq.bed) that contains “queryID queryStart queryEnd”. Following is the example (the content of seq.bed file). SRR5892231.6 28 178 SRR5892231.7 4 307 SRR5892231.7 16 307 SRR5892231.9 216 408 I would like to…

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GATK HaplotypeCaller – Shutting down engine

00:32:48.224 INFO  HaplotypeCaller – Shutting down engine [September 17, 2021 12:32:48 AM CST] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 0.04 minutes. Runtime.totalMemory()=2398617600 java.nio.BufferUnderflowException         at java.nio.ByteBuffer.get(ByteBuffer.java:688)         at java.nio.DirectByteBuffer.get(DirectByteBuffer.java:285)         at java.nio.ByteBuffer.get(ByteBuffer.java:715)         at htsjdk.samtools.MemoryMappedFileBuffer.readBytes(MemoryMappedFileBuffer.java:34)         at…

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How can I find reads for specific elements in a bam file?

Hi, I have a specific set of 1,009 elements in a bed file that I am interested in. I also have bam files which I would like to process to know the number of reads for these specific elements (for comparison purposes). I understand some simple uses of samtools commands,…

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converting Bam to fastq while removing clipping(hard/soft clip bases)

converting Bam to fastq while removing clipping(hard/soft clip bases) 0 Hello, I want to do some analysis and my raw data is paired-end reads fastq files. So far: I used BWA mem to convert them to Sam file then used samtools to convert to BAM file. My next step is…

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