Tag: SAM

How good is Genozip at compressing BAM files? ​ See Benchmarks. ​ Compressing a BAM, SAM or CRAM file  ​ In the rest of this page we will give examples of BAM files. Genozip is also capable of compressing SAM files, and with some limitations, CRAM files as well. ​…

Javascript is currently disabled or is not supported by this browser. Please enable JavaScript for full functionality. Sorry, there was a problem loading sequence from server. Please try again and contact us if the problem persists. Automated summary: This ncRNA sequence is 53 nucleotides long and is found in Candidatus…

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Hi guys, I seem to have run into this error and I’m not sure why. Any suggestions to fix this? I have already deleted the data and downloaded the files again and am still running into the issue. I am running qiime2-2022.8 qiime demux summarize \ –i-data /Users/sam/LT-paired-ends.qza –o-visualization LT-paired-ends.qzv…

Samtools Convert Sam To Bam With Code Examples In this session, we’ll try our hand at solving the Samtools Convert Sam To Bam puzzle by using the computer language. The code that follows serves to illustrate this point. # Basic syntax: samtools view -S -b sam_file.sam > bam_file.bam # Where:…

separate read1 and read2 from merged fastq file and align against reference genome 0 Hi, I am processing a merged fastq file. I used the following command to separate read1s and read2s in separate files for alignment using bwa mem. paste – – – – – – – – <…

PRSice-2 Documentation 1 Hi, Does anyone has detailed documentation of PRSice-2 software? The official website has been down for several weeks. Thank you! Mengna PRSice-2 • 69 views We lost the domain name because we forgot the login password… You can now revert to the repo doc (which is the…

I am working with Illumina GAII derived mate pair data. I am attempting to identify two things in the sequences so that I can get rid of spurious data: 1. Are the reads rf or fr. I know picard must have the ability to identify this info from a sam…

Name Last modified Size Description Parent Directory   –   cram.h 2015-06-24 11:00 2.4K   cram_codecs.c 2017-09-26 09:28 50K   cram_codecs.h 2016-03-17 07:48 6.0K   cram_codecs.o 2018-03-04 16:57 175K   cram_decode.c 2018-01-26 05:33 84K   cram_decode.h 2013-10-16 06:15 3.4K   cram_decode.o 2018-03-04 16:57 236K   cram_encode.c 2017-07-03 16:45 87K  …

Bedtools Bam To Bed With Code Examples With this article, we’ll look at some examples of how to address the Bedtools Bam To Bed problem . bedtools bamtobed [OPTIONS] -i <BAM> As we have seen, a large number of examples were utilised in order to solve the Bedtools Bam To…

align kmers to reference genome 0 dear all, I have a fasta file with a list of 25-mers and I am trying to align it to the reference genome ref.fa using bowtie2 I did bowtie2 -x ref -f ref_25mers.fa -S ref_25mers.sam but it gives the result 1 reads; of these:…

HISAT2 and HTSEQ command 0 @4fedfa78 Last seen 10 hours ago Japan Hello, For analysis of the data by rna-sequencing I selected HISAT2 and HTSeq-count for mapping and counting the genes levels, the libraryLayout is paired, I am using the below command for both but the results are not exact…

Hi everyone- I am trying to write a script to automate htseq-count on a large number of samples. The script runs but then throws the following error: “Please provide 2 arguments”. Does anyone see something obvious I am missing: #!/bin/bash for samples in *.sam do gtf = “Galaxy135-\[Escherichia_coli_str_k_12_substr_mg1655.GCA_000005845.2.29.gtf\].gtf” echo $sample …

Selection of naturally occurring human SARM1 variants with potential for LoF We hypothesised that naturally occurring SARM1 coding variation that confers LoF exists in the general human population. Previous studies have shown that disruption of the SAM multimerization domains or catalytic TIR domain of SARM1 is more likely to cause…

Name Last modified Size Description Parent Directory   –   bgzf.h 2018-01-10 07:45 14K   cram.h 2015-09-25 05:36 15K   faidx.h 2017-02-07 11:06 5.6K   hfile.h 2018-01-26 05:33 9.6K   hts.h 2017-11-24 09:46 29K   hts_defs.h 2017-08-10 11:07 3.3K   hts_endian.h 2017-09-27 10:40 11K   hts_log.h 2017-06-03 15:45 3.8K  …

Name Last modified Size Description Parent Directory   –   HmmGlocal.java 2014-08-01 09:48 9.0K   ace2sam.c 2016-05-10 08:11 11K   blast2sam.pl 2017-09-14 10:20 5.2K   bowtie2sam.pl 2014-08-18 14:29 3.3K   export2sam.pl 2014-08-01 09:48 18K   interpolate_sam.pl 2014-08-18 14:29 6.0K   maq2sam.c 2017-12-12 11:10 7.2K   md5fa.c 2017-07-24 09:15 2.8K  …

In this tutorial we learn how to install libhts-dev on Kali Linux. libhts-dev is development files for the HTSlib Introduction In this tutorial we learn how to install libhts-dev on Kali Linux. What is libhts-dev HTSlib is an implementation of a unified C library for accessing common file formats, such…

Could not locate a HISAT2 index to basename 2 First time trying out HISAT2 and I’m having a problem here, even with the pre-made indices for GRCH38. $ hisat2 -x /share/projects/RNASeq/data/reference/GRCh38/grch38_tran -1 /home/echang/PANCANCER-030817-JE3-35880845/KTP-10-43736695/KTP-10_S3_L001_R1_001.fastq.gz -2 /home/echang/PANCANCER-030817-JE3-35880845/KTP-10-43736695/KTP-10_S3_L001_R2_001.fastq.gz -S tmp.sam Error follows Could not locate a HISAT2 index corresponding to basename “/share/projects/RNASeq/data/reference/GRCh38/grch38_tran” Error:…

Issue Title State Comments Created Date Updated Date How to get a specific chromosome open 1 2022-07-14 2022-07-18 tabix returns row from VCF file multiple times open 4 2022-07-11 2022-07-18 Modified base parsing failure failure closed 0 2022-07-01 2022-07-18 extract genotype information open 1 2022-06-24 2022-07-18 sam_hdr_remove_lines is inefficient if…

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AlphaFold: The making of a scientific breakthrough The inside story of the DeepMind team of scientists and engineers who created AlphaFold, an AI system that is recognised as a solution to “protein folding”, a grand scientific challenge for more than 50…

Software official website ： Hisat2： Manual | HISAT2 StringTie：StringTie article ：Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown | Nature Protocols It is recommended to watch the nanny level tutorial ： 1. RNA-seq : Hisat2+Stringtie+DESeq2 – Hengnuo Xinzhi 2. RNA-seq use hisat2、stringtie、DESeq2 analysis – Simple books Basic usage…

Issue Title State Comments Created Date Updated Date Mapping reads against multi references. Any proposition? open 0 2022-06-28 2022-06-30 Inversion between tandem repeats yields misalignment closed 1 2022-06-21 2022-06-30 use minimap2 to extract mitochondrial reads from genome assembly open 0 2022-06-20 2022-06-30 Asking for #301 to be reopened closed 0…

extract rRNA/tRNA and other ncRNA ratio in a table from small RNA-seq 0 Hi all, I have some small RNA-seq libraries from some plants. I downloaded ncRNA from Ensemble Plants as I don’t know how to use the Rfam database. How could I extract the rRNA/tRNA and other ncRNA ratios…

Provided by: biobambam2_2.0.179+ds-1_amd64 NAME bamfillquery – fill query sequences into BAM files SYNOPSIS bamfillquery [options] <in.bam queries.fasta >out.bam DESCRIPTION bamfillquery reads a SAM/BAM/CRAM file and a FastA file, copies the sequences found in the FastA file into the query sequence field of the SAM/BAM/CRAM file and writes the resulting data…

ID A0A6I9ZUN5_ACIJB Unreviewed; 234 AA. AC A0A6I9ZUN5; DT 07-OCT-2020, integrated into UniProtKB/TrEMBL. DT 07-OCT-2020, sequence version 1. DT 25-MAY-2022, entry version 6. DE SubName: Full=tumor necrosis factor ligand superfamily member 8 {ECO:0000313|RefSeq:XP_014931799.1}; GN Name=TNFSF8 {ECO:0000313|RefSeq:XP_014931799.1}; OS Acinonyx jubatus (Cheetah). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; OC Eutheria; Laurasiatheria;…

Provided by: samtools_1.13-2_amd64 NAME samtools targetcut – cut fosmid regions (for fosmid pool only) SYNOPSIS samtools targetcut [-Q minBaseQ] [-i inPenalty] [-0 em0] [-1 em1] [-2 em2] [-f ref] in.bam DESCRIPTION This command identifies target regions by examining the continuity of read depth, computes haploid consensus sequences of targets and…

Extract R1 and R2 from sam file generated by bowtie2 1 Hi every one How to extract R1 and R2 from sam file generated by bowtie2 ? sam bowtie2 samtools bam • 137 views • link updated 14 hours ago by iraun &starf; 4.4k • written 15 hours ago by…

Read counts an order of magnitude higher on one chromosome 3 Hi, I am having an issue with a sequencing run that when demultiplexed, aligned, and filtered each individual has 1-2 million reads, but these reads are predominantly on one chromosome. For background these are oncorhynchus mykiss and o. clarki…

3 month , My first post in the new student group , The false-positive mutation appears because duplicates mark Not enough ？, Tells the story of supplementary read It won’t be GATK MarkDuplicates Marked as duplicates The problem of . after , In response to this question , I began…

Newbie here. Please, play nice. I got possession of a set of 4 .bam files that stores the exome of an individual, around 400 MB each. I used samtools to generate a 2.4 GB .sam file out of one of the .bam files, and I found it contains lines with…

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Running fastqc 1 I am trying to run fastqc from my home directory using the command line. I do not have access to the root directory. I have downloaded fastqc zip file and unzipped it. When going into the FastQC directory, the following options are available: Configuration, LICENSE_JHDF5.txt, cisd-jhdf5.jar, net…

bowtie2 – (ERR): bowtie2-align exited with value 13 1 I am trying to run bowtie2. but following error are occuring everytime bowtie2 –very-fast-local -x bowtie -q -1 R1.fastq -2 R2.fastq -s aligned.sam Saw ASCII character 10 but expected 33-based Phred qual. terminate called after throwing an instance of ‘int’ Aborted…

Split merged Bam file without replacement 0 Hi guys, I have 5 bam (ChIPseq PE data sorted by position) files that came from 5 different murine cortexes (mice that belong to the same group, so biological replicates), however I have a lot of group variability. I’m thinking to merge all…

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Hello, I would like to confirm if the low assignment ratio (54%) is normal, and please check the possible reason I found. I used Hisat2 to assign paired-end strand-specific transcriptomic sequences (rRNA removed) to a reference genome. Because I filtered out the unmapped sequences in advance, the overall assignment ratio…

Filtering bam file based on depth determined through samtools depth 1 Hi All, I have a bam file and I calculated read depth using samtools depth and I now want to filter the bam file to have only the contigs that have a depth between a certain value. I was…

Let me preface this with the admission that I am not an “expert” here by any means, which means I’m learning as I’m going. I have been tasked with the analysis of high dimensional (spectral) flow cytometry data with 32 parameters (time, six linear parameters (FSC and SSC) and 24…

Dear all, It writes the following in the log file: [08-02 01:26:25] Running Step 2: BWA … bwa_wrap /work/pathology/s206442/dbet_project/hg19/hg19.fa Output3/out_1.valid.fastq 6 Output3/out_1.valid.sam 0 Running BWA on trimmed reads … bwa mem -t 6 /work/pathology/s206442/dbet_project/hg19/hg19.fa Output3/out_1.valid.fastq | samtools view -h -F 2048 – > Output3/out_1.valid.sam However, the sam file size is…

Currently, unmapped reads are included in the SAM file. I have a scenario where 99% of the reads won’t map to the reference sequences used (i.e. mapping only to a gene family). This creates unnecessarily large files which need to be filtered to reduce their size (e.g. sed). It’d be…

How to edit a SAM file using pysam 0 Dear all – I have a template sam file and I want to change one of the columns (template_length) and replace it with a new value. The new value is a quick mathematical operation. template sam file: @HD VN:1.0 SO:unsorted @SQ…

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Sam50 is a key component of the sorting and assembly machinery (SAM) complex and is also involved in bridging mitochondrial outer and inner membrane contacts. However, the physiological and pathological functions of Sam50 remain largely unknown. On March 21, 2022, Wuhan University Song Zhiyin and Meng Qingtao jointly published a…

Messages in this thread Subject Re: [PATCH v4 3/3] drm/bridge: ti-sn65dsi86: Support hotplug detection From Kieran Bingham <> Date Wed, 23 Mar 2022 22:11:25 +0000 Quoting Doug Anderson (2022-03-23 21:47:17)> Hi,> > On Thu, Mar 17, 2022 at 6:13 AM Kieran Bingham> <kieran.bingham+renesas@ideasonboard.com> wrote:> >> > @@ -1241,9 +1350,32 @@…

subsample fasta to certain size 1 Hi there, Can anyone suggest a tool or method to extract random 10GB reads with minimum read length of (1000bp) from a huge 100 Gb file. I have 50 different fa.gz files with varying size (20 -100GB) and I like to subsample fasta with…

Why did I achieve shorter than initial reads subset after aligned reads extraction. 1 Hello dear colleages! I have recently faced some problem. I have worked with long WGS reads. Firstly I have filtered the longest subset of reads, and aligned them to the custom sequence with several structural variants…

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Feature count is very low using htseq-count 0 Hello all, I performed bbmap on my RNA-seq paired sequence data using following cmd bbmap.sh in1=J2_R1.fastq in2=J2_R2.fastq out=output_J2.sam ref=im4.fasta nodisk The header of generated sam file is @HD VN:1.4 SO:unsorted @SQ SN:k141_1006 LN:2503 @SQ SN:k141_5512 LN:5393 @SQ SN:k141_4772 LN:4387 @SQ SN:k141_3267 LN:4531…

Minimap2 options for Nanopore cDNA direct seq 0 Hello, I’m working with ONT RNA seq data and I used the cDNA direct seq to do the seq. I want to look for long deletions in mRNAs that are not spliced, for this, I want to use the splice option of…

Once you already have your phyloseq object df_family, you can use the function estimate_richness from phyloseq. You can then join the sample meta data to this data frame of alpha diversities. Finally, you can use ggplot2 directly to customize your plot accordingly, e.g. to put different sample groups (here SampleType)…

%PDF-1.5 % 211 0 obj > endobj 295 0 obj >stream application/pdf Snaq: A Dynamic Snakemake Pipeline for Microbiome data analysis with QIIME2 2022-03-11T02:09:25Z LaTeX with hyperref 2022-03-13T05:02:28-07:00 2022-03-13T05:02:28-07:00 pdfTeX-1.40.23 False This is pdfTeX, Version 3.141592653-2.6-1.40.23 (TeX Live 2021) kpathsea version 6.3.3 uuid:4f5ae20a-1dd2-11b2-0a00-300927edca00 uuid:4f5ae20e-1dd2-11b2-0a00-380000000000 endstream endobj 212 0 obj > endobj…

Provided by: sambamba_0.8.2+dfsg-2_amd64 NAME sambamba-view – tool for extracting information from SAM/BAM files SYNOPSIS sambamba view OPTIONS <input.bam | input.sam> [region1 […]] DESCRIPTION sambamba view allows to efficiently filter SAM/BAM files for alignments satisfying various conditions, as well as access its SAM header and information about reference sequences. In order…

That kind of custom fiddling with reads and variants is very cumbersome, non-standard and also error-prone. Do a standard variant callign pipeline and then filter for the mutations that you want. Then extract the variant position (so the coordinates) and get the variant context from the reference genome. Using individual…

AllHigh-Throughput SequencingGenomicsProteomicsVisualizationOther BBTools Description a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data. BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw, with autodetection of quality encoding and interleaving. Installation Use the following command to…

I am struggling with samtools index. I already did the alignment using “bwa mem reference.fa seq.fastq > alg.sam”. The resulting sam file was converted to bam format using “samtools view -S -h -b alg.sam > alg.bam”. Next, the files were sorted by using “sort -h alg.bam >sorted.bam”. And now we…

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When I tried to use samtools to split a bam file based on different chromosomes, I used this command: samtools view input.bam -b chr21 | chr21.bam However, I get error messages like this: -bash: chr21.bam: command not found [W::hts_idx_load3] The index file is older than the data file: input.bam.bai How…

SAMSequenceRecord JavaScript is disabled on your browser. All Implemented Interfaces: java.io.Serializable, java.lang.Cloneable public class SAMSequenceRecord extends AbstractSAMHeaderRecord implements java.lang.Cloneable Header information about a reference sequence. Corresponds to @SQ header record in SAM text header. See Also: Serialized Form Field Summary Fields  Modifier and Type Field and Description static java.lang.String ASSEMBLY_TAG …

I am creating a threaded c++ file where i generate in silico bam files, using header, DNA sequence and read information. First i use bam_init1() to create the bam1_t structure just named “b”. Then i use bam_set1 to create the actual sequence entry in the bam file bam_set1(b,read_id_length,READ_ID,flag,chr_idx,min_beg,mapq,n_cigar,cigar,-1,-1,0,strlen(DNAsequence),DNAsequence,quality_string,l_aux) And finally…

ID A0A1S3QEZ7_SALSA Unreviewed; 104 AA. AC A0A1S3QEZ7; DT 12-APR-2017, integrated into UniProtKB/TrEMBL. DT 12-APR-2017, sequence version 1. DT 02-JUN-2021, entry version 11. DE SubName: Full=lipopolysaccharide-induced tumor necrosis factor-alpha factor homolog isoform X2 {ECO:0000313|RefSeq:XP_014038412.1}; GN Name=LOC106591717 {ECO:0000313|RefSeq:XP_014038412.1}; OS Salmo salar (Atlantic salmon). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Actinopterygii;…

because the CIGAR in bam/sam file generated by minimap2 contain “=” , represent right match with reference, and “X”, represent wrong match with reference. while the bam_cigar.py in ./lib/qcmodule/bam_cigar.py only suit for bam/sam generated such as BWA/bowtie, which CIGAR contain only “M” ,represent mis/match. So i modified the bam_cigar.py 77…

I am trying to create an automatic chain of commands for analyzing biological data. For this I am using Samtools in Slurm cluster. This line below is one of the commands I run for the analysis: samtools view -h file.sam | awk ‘$6 ~ /N/ || $1 ~ /^@/’ |…

Difference of results with the same input [RNAseq analysis] 0 Hello! I am trying to optimize the treatment of some RNAseq files by splitting the input reads into several files. I am comparing the results I have obtained with: the reads input as one file the split input as several…

[PATCH v1 5/9] drm/bridge: ti-sn65dsi86: Fetch bpc via drm_bridge_state – Sam Ravnborg From: Sam Ravnborg <sam@ravnborg.org> To: dri-devel@lists.freedesktop.org, Douglas Anderson <dianders@chromium.org> Cc: Rob Clark <robdclark@chromium.org>, Philip Chen <philipchen@chromium.org>, Jitao Shi <jitao.shi@mediatek.com>, Thomas Zimmermann <tzimmermann@suse.de>, Jonas Karlman <jonas@kwiboo.se>, Robert Foss <robert.foss@linaro.org>, Neil Armstrong <narmstrong@baylibre.com>, Jernej Skrabec <jernej.skrabec@gmail.com>, Andrzej Hajda <a.hajda@samsung.com>, Laurent…

Hu @FadelBerakdar, Indeed, you can get true positive and false positive alignments in output. You have to specify the files where this information will be stored under the files section of a given software output. The output format is SAM files without headers. The name given in parameter is just…

Not only will you save disk space by converting to BAM, but BAM files are faster to manipulate than SAM. Source: Dave Tang’s SAMTools wiki. sort supports uncompressed SAM format from a file or stdin, though index requires BGZIP-compressed SAM or BAM. I don’t think you can get around this….

bwa , 2 files fastq to 1 sam 1 i have this problem, please, help me, I’m trying it too from Mac OS Catalina I am creating a sam file, with 2 fastq files, using bwa I apply the following command bwa mem -t 2 GRCh38.primary_assembly.genome.fa.gz V350019555_L03_B5GHUMqcnrRAABA-556_1.fq.gz V350019555_L03_B5GHUMqcnrRAABA-556_2.fq.gz > V350019555_L03_B5GHUMqcnrRAABA-556.sam…

I have some RNAseq data from miRNAs that I have processed with Bowtie2 (aligning to miRBase). Now, when doing the deduplication with umi_tools dedup I find that some of the files take a lot of time+RAM to finish (some files take around 3-4 minutes and 4-5GB of RAM and some…

Provided by: samtools_1.13-2_amd64 NAME samtools reheader – replaces the header in the input file SYNOPSIS samtools reheader [-iP] [-c CMD | in.header.sam ] in.bam DESCRIPTION Replace the header in in.bam with the header in in.header.sam. This command is much faster than replacing the header with a BAM→SAM→BAM conversion. By default…

Unable to convert from sam to bam file. 0 samtools view -S -b BD143_TGACCA_L005.sam -o BD143_TGACCA_L005.bam When I am running this command the following error is appearing: [main_samview] fail to read the header from “BD143_TGACCA_L005.sam”. As a result, if anyone knows how to fix this error and thanks. converting File…

samtools sort 1 I am transforming sam files to bam, to facilitate their ordering I use this command, % cd /Volumes/GENOMA/BWA % samtools sort -n -O V350019555_L03_B5GHUMqcnrRAABA-551.sam | samtools fixmate -m -O bam V350019555_L03_B5GHUMqcnrRAABA-551.bam but it gives me the following error, As elsewhere in samtools, use ‘-‘ as the filename…

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HKEY_LOCAL_MACHINE/SECURITY contains information about the machine’s security. Account information, including cached login credentials,, is supposedly stored in the cache. Additionally, the SAM database is also stored here, though it is protected from write access. where does microsoft stores user security information – Related Questions Where does Windows store user information?…

The true power of the state space model is to allow the creation and estimation of custom models.This notebook shows various statespace models that subclass sm. That means your MAGeCK python module is installed in /home/john/.pyenv/versions/2.7.13/lib/python2.7/sitepackages.I use conda to install the latest version of. This twovolume set Diseases and Pathology…

Hi Guys, When I am trying to run bwa mem on multiple processor, I am getting error as : > mpirun -np 16 bwa mem hg19-agilent.fasta R1.fastq R2.fastq | samtools sort -o aln.bam [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::bwa_idx_load_from_disk] read…

Samtools flagstat 1 I aligned my ONT sequencing run with minimap2, subsequently I filtered the file using samtools view -b -F 256 aln_transcriptome_sorted_6.bam -o filtered_aln_transcriptome_6.bam to end up with primary alignments only. When I run samtools flagstat on the filtered file I get the following output: 3502608 + 0 in…

Polygenic Risk Score Calculation: Do we need to apply the same p-value threshold on all 22 chromsomes? 1 Hi there, I am using PRSice-2 to calculate the polygenic risk score for 22 chromosomes one by one. To my understanding, since the 22 chromosomes are independent of each other, and our…

tranfering sam file easy and fast way 0 Hi everyone I was tried to align my fastq files by hisat2 but ı couldnot able done because my computer has 4gb ram and ı get error killed. So ı was perfomed process on my friend computer but now I should solve…

Hello, I’m following the htseq-count tutorial for RNA-seq (counting the overlapping genes and exons) here htseq.readthedocs.io/en/master/tour.html. However, when I get to the point where I need to find the overlaps in the .sam file and .gtf file, I get an error. This is the code I ran originally that gave…

featureCounts output has letters and +/- sign 1 Hello, I have created a featureCounts table and 10 of my files had weird outputs. Some values were my organism name and others were a “+” or “-“. I could not find anything about this in the manual. I tried to re-run…

samtools sorts allocate memory for bam_mem issues 1 Hello everyone ı am trying to convert sam to bam samtools sort -@ 8 -o UHR_Rep1.bam UHR_Rep1.sam and ı got this error samtools sort: couldn’t allocate memory for bam_mem ı check my disk memory and ı see have enough space in my…

[*] I have been trying to follow the GATK Best Practice Workflow for ‘Data pre-processing for variant discovery’ (gatk.broadinstitute.org/hc/en-us/articles/360035535912). This has all been run on Windows Subsystem for Linux 2 on the Bash shell. I started off with FASTQ files from IGSR (www.internationalgenome.org/data-portal) and performed alignment with Bowtie2 (instead of…

BLEND is a mechanism that can efficiently find fuzzy seed matches between sequences to significantly improve the performance and accuracy while reducing the memory space usage of two important applications: 1) finding overlapping reads and 2) read mapping. Finding fuzzy seed matches enable BLEND to find both 1) exact-matching seeds…

Which is @RG read group in the head of bam files? 1 I am not sure which part of the head of bam files is @RG read group. I am curious why all of my samples have the sameA01494:44:H53Y7DMXY:1 part? Are they read groups? samtools view -S Sample_7R-MDV_IGO_09530_H_1_dedup.bam | head…

Hello, I am working with bifacial modules,  To investigate the effect of the distance between the panels on the energy produced, I changed the GCR, expecting this factor to be ineffective for very long distances because it has practically no effect on the shadow, for example for 50 meters, and…

Hello Team, I am not able to test springboot applilcation with AWS lambda in my local using SAM CLI, because it generates classes with very long names , which the SAM Cli is not able to copy tom tmp folder, when deploying as a docker container and I get an…

samtools mpileup error – 1 samples in 1 input files 0 Hi All, I have relatively new to bioinformatics and have encountered an issue when trying to generate an mpileup file with samtools. I have entered the following command samtools mpileup -f /home/path_to_reference/nCoV_Jan31.fa.fasta sorted_sample1.sam > sample.mpileup The message returned is…

How can I make sure certain SNPs are not removed during the clumping stage of PRS calculation using PRSice 1 This is a two part question. First, when implementing PRSice, is there a way to make sure certain SNPs are retained for the PRS calculation? I basically want to avoid…

Attempting to generate a bam.bai file but the output is not readable 1 Hi, I am new a exome sequencing, and have tried to follow tutorials on the subject. I am stuck at the samtools index stage because the output files are in a non-human readable format and I believe…

(ERR): hisat2-align died with signal 6 (ABRT) (core dumped) 0 Hi, run hisat2 ,I encountered an error. hisat2-build -p 10 ~/public_data/genome/Pt_V1.0.fa genome 1>hisat2-build.log 2>&1 ~/software/hisat2-2.2.0/hisat2 -x genome -1 ~/data/clean/NC1_5_clean_R1.fastq.gz -2 ~/data/clean/NC1_5_clean_R2.fastq.gz -S NC1_5.sam 1>NC1_5.log 2>&1 cat NC1_5.log terminate called after throwing an instance of ‘std::bad_alloc’ what(): std::bad_alloc (ERR): hisat2-align died…

BBSplit ambiguous dataset analysis 1 I have used bbsplit to split a metagenomic dataset into reads mapping to three genomes a, b, c. bbsplit.sh in1={fastq_1} in2={fastq_2} ref={ref_str} ambiguous2=split basename={out_path}out_split_%.sam If I want to identify which ambiguous reads align to ‘a’ and any other genome – is this only ‘ambiguous_a’? or…

I’ve got sequencing data for a small 500 bp amplicon from a few samples. GATK best principles suggest running VariantRecalibrator on the GVCF files I generate. I’m trying to get this working, but I get an error about “Found annotations with zero variances”. Reading the gatk manual and other posts…

Why single cell R2 fastq have no read identified by bowtie2 ? 0 When we input R2 fastq.gz into bowtie2, human sequence was not removed ( ${base}_host_removed is zero). for i in $(find ./ -type f -name “.fastq.gz” | while read F; do basename $F | rev | cut -c…

I’ve managed to define a template for a Lambda behind an API GW authenticated via (dedicated) ApiKey by describing everything in the template and with no OpenApi definition. The problem arises when trying to introduce Lambda Integrations for accomplishing the mappings: it seems that they can be defined only in…

htseq-count Error ‘_StepVector_Iterator_obj’ object has no attribute ‘next’ 0 I am trying to run htseq-count (v. 0.13.5) on a sorted and indexed bam file. The command I entered looks like this: htseq-count -f bam -r pos -s yes -t CDS -i gene_id -m union filename_sorted.bam filename.gtf I get the following…

Inscripta was founded in 2015 and recently launched the world’s first benchtop Digital Genome Engineering platform. The company is growing aggressively, investing in its leadership, team, and technology with a recent $150mm financing round led by Fidelity and TRowe price. The company’s advanced CRISPR-based platform, consisting of an instrument, reagents,…

Hello, I’m following the htseq-count tutorial for RNA-seq (counting the overlapping genes and exons) here htseq.readthedocs.io/en/master/tour.html. However, when I get to the point where I need to find the overlaps in the .sam file and .gtf file, I get an error. This is the code I ran originally that gave…

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…

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…