Tag: SAM

extract rRNA/tRNA and other ncRNA ratio in a table from small RNA-seq

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…

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Ubuntu Manpage: bamfillquery – fill query sequences into BAM files

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…

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UniProt: A0A6I9ZUN5_ACIJB

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;…

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Ubuntu Manpage: samtools targetcut – cut fosmid regions (for fosmid pool only)

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…

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Extract R1 and R2 from sam file generated by bowtie2

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…

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Read counts an order of magnitude higher on one chromosome

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…

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Detailed differences between sambamba and samtools

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…

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BAM file and no RNAME or POS information? : bioinformatics

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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genetic epidemiology postdoc

Qualification Details. Objective/methods: This report investigates by histology, immunohistochemistry and in situ hybridization the histological and . Philip Lupo, Ph.D. Dr. Lupo is a co-principal investigator in the Systems Epidemiology of Cancer Training Program and an associate professor in the Section of Hematology-Oncology in the Department of Pediatrics. . «Genetic…

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Running fastqc

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…

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(ERR): bowtie2-align exited with value 13

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…

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Split merged Bam file without replacement

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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FGFR2 antibody | Axil Scientific

This website uses cookies to ensure the best experience. By continuing, you agree to our privacy policy. × Product successfully added to quote! × There are items in your quote. Brand: Reference GTX10647 Brand GeneTex Application IHC-PWB Storage Conditions Store as concentrated solution. Centrifuge briefly prior to opening vial. For…

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The low successful assignment ratio of FeatureCounts

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…

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Filtering bam file based on depth determined through samtools depth

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…

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L-BFGS-B needs finite values of ‘fn’

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…

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Sam file is not written

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…

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Option To Exclude Unmapped Reads From SAM

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…

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How to edit a SAM file using pysam

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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dCas9-VP64-Blasticidin SAM CRISPRa Helper Construct 1 Plasmid DNA

This product is a lentiviral plasmid that utilizes the EF1 alpha promoter to drive expression of dCas9-VP64 and blasticidin resistance cassette linked by a 2A peptide (EF1a-dCas9-VP64-2A-Blasticidin) allowing for easy selection following successful transfection or transduction. Use Sigma′s lentiviral dCas9-VP64 plasmid for generation of lentiviral particles and efficient production of…

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Wuhan University Song Zhiyin and other teams discovered a new mechanism of mitochondrial DNA release

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…

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LKML: Kieran Bingham: Re: [PATCH v4 3/3] drm/bridge: ti-sn65dsi86: Support hotplug detection

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 @@…

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subsample fasta to certain size

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…

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Why did I achieve shorter than initial reads subset after aligned reads extraction.

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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Sarah Dash’s Bio, Net Worth, Height, Facts, Career

Sarah Dash was an accomplished American singer and actress who was recognized for her work with the band LaBelle and as a studio musician for musicians such as The Rolling Stones. She rose to prominence as a solo singer thanks to tracks like “Sinner Man,” a Top 10 disco hit….

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Feature count is very low using htseq-count

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…

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Minimap2 options for Nanopore cDNA direct seq

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…

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ggplot2 – Fail to plot by group on a phyloseq object generated by R package Divnet

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)…

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A Dynamic Snakemake Pipeline for Microbiome data analysis with QIIME2

%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…

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Ubuntu Manpage: sambamba-view – tool for extracting information from SAM/BAM files

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…

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bam – Detect mutation context in a read of a sam file

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…

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BBTools – BioGrids Consortium – Supported Software

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…

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sorting – indexing sorted alignment file with samtools index gives “Exec format error”

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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Galaxy Genome [Space Sim] HACK/MOD Unlocked All vVaries with device

Download Galaxy Genome [Space Sim] Mod Varies with device for android apk & iphone ios 4.4 and up Galaxy Genome is an open world sci-fi space simulator. You can upgrade your ship and customize each component as you hunt, explore, fight, mine, smuggle, trade and survive in a brutal galaxy….

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bam – samtools view command not found error

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…

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SAMSequenceRecord

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 …

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sam – Use Htslib to create auxilary tags in bam file C++

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…

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UniProt: A0A1S3QEZ7_SALSA

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;…

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[MonashBioinformaticsPlatform/RSeQC] junction_saturation not suit for bam/sam file generated by minimap or pbmm2

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…

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awk – Submitting a job in Slurm using wrap

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 ~ /^@/’ |…

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Difference of results with the same input [RNAseq analysis]

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…

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[PATCH v1 5/9] drm/bridge: ti-sn65dsi86: Fetch bpc via drm_bridge_state

[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…

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How to separate true positive alignments from a given SAM file

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…

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samtools – How to Sort and Index a SAM file without converting it to BAM?

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….

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bwa , 2 files fastq to 1 sam

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…

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UMItools dedup deduplication taking too much time + RAM

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…

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Ubuntu Manpage: samtools reheader – replaces the header in the input file

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…

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Unable to convert from sam to bam file.

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…

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samtools sort

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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PyTorch’s Cult Following

PyTorch’s popularity spread only three years after its launch: the open-source ML library posted a 194% user growth in the first half of 2019. Since then PyTorch has not looked back. According to the survey by Stackoverflow, while TensorFlow is the most in-demand library, PyTorch is more preferred. Data from…

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where does microsoft stores user security information?

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?…

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Mle Application With Gekko In Python

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…

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Bwa on multiple processor

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…

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Samtools flagstat

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…

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Do we need to apply the same p-value threshold on all 22 chromsomes?

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…

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tranfering sam file easy and fast way

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…

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htseq-count python tutorial attribute counts error

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…

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featureCounts output has letters and +/- sign

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…

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samtools sorts allocate memory for bam_mem issues

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…

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sequence alignment – MarkDuplicatesSpark failing with cryptic error message. MarkDuplicates succeeds

[*] 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…

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A Fast, Memory-Efficient, and Accurate Mechanism to Find Fuzzy Seed Matches

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…

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Which is @RG read group in the head of bam files?

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…

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effect of GCR on energy production – SAM Forum

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…

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Issue with running SpringBoot Application using AWS Lambda in SAMCLI

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…

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samtools mpileup error – 1 samples in 1 input files

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…

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How can I make sure certain SNPs are not removed during the clumping stage of PRS calculation using PRSice

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…

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Attempting to generate a bam.bai file but the output is not readable

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…

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hisat2-align died with signal 6 (ABRT) (core dumped)

(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…

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BBSplit ambiguous dataset analysis

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…

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Padding out a GVCF file with 1000G exomes to get gatk VariantRecalibrator working with a small sample

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…

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Why single cell R2 fastq have no read identified by bowtie2 ?

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…

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AWS SAM :: AWS::Serverless::Api “Invalid value for ‘Auth’ property”

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…

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htseq-count Error ‘_StepVector_Iterator_obj’ object has no attribute ‘next’

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…

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Senior Bioinformatics Scientist II/ Staff Bioinformatics Scientist

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,…

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HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.

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…

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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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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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Chunk

Chunk JavaScript is disabled on your browser. All Implemented Interfaces: java.io.Serializable, java.lang.Cloneable, java.lang.Comparable<Chunk> public class Chunk extends java.lang.Object implements java.lang.Cloneable, java.io.Serializable, java.lang.Comparable<Chunk> A [start,stop) file pointer pairing into the BAM file, stored as a BAM file index. A chunk is represented as a single 64-bit value where the high-order 48…

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Proximo DNA Sequencing and Hi-C Library Preparation – ABL-21058B, Missouri

**AMENDMENT TO EXTEND SOLICITATION DATE ** This is a combined synopsis/solicitation for services in which the government intends to acquire in accordance with FAR Part 13, Simplified Acquisitions Procedures. Department of Commerce (DOC), National Oceanic & Atmospheric Administration (NOAA), National Marine Fisheries Service (NMFS), Alaska Fisheries Science Center, Auke Bay…

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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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bowtie2-align died with signal 24 (XCPU) (core dumped)

(ERR): bowtie2-align died with signal 24 (XCPU) (core dumped) 0 Hi all, it is my first time using bowtie2, and I have a problem. I conducted the following command for reads mapping: bowtie2 -q –local -x mm10 -U SRR5839956_trimmed.fq -S SRR5839956.sam It created a 600MB sam file then come with…

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How to extract unique mapped results from Bowtie2 bam results?

How to extract unique mapped results from Bowtie2 bam results? I used samtools view -bq 1 WG.bam > unique.bam However, my results contain 54792 lines, why it is not 42097?   After I have the subset of those reads, how can I extract them from sam or bam file to create a…

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Dnaman software manual

Dnaman software manual DNADynamo DNA Sequence Analysis SoftwareCLC Genomics Workbench – Qiagen They have sent a man to locate the key. He was making notes with a slim gold pen on a Gucci pad? When I married my husband, that all…

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The sardine run in southeastern Africa is a mass migration into an ecological trap

INTRODUCTION Large-scale annual migrations occur in an extraordinary range of animals, from insects to the great whales. While the driving mechanisms of these migrations are varied and sometimes poorly understood, they often represent a way of optimizing conditions for breeding and adult fitness when these are in conflict. Often, populations…

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Align fastq SOLiD data

Align fastq SOLiD data 1 Hello everyone, I have downloaded some data from the short read archive using the sratoolkit. The data is SOLiD data. I have seen people using the Lifescope (Life Technologies) to align the reads, as I presume it works for this type of data. But unfortunately,…

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PRS using PGS Catalog

PRS using PGS Catalog 1 When using PRSice for PRS calculation of target data using a file of variants from the PGS catalog, does the variant file from the PGS catalog replace the GWAS summary statistics (referred to as “base data” in the tutorial)? I had previously found this similar…

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PRS in UK Biobank – no covariate file and no phenotype file

PRS in UK Biobank – no covariate file and no phenotype file 1 Hi there, I am trying to undertake a PRS using UK Biobank plink data. I am trying to generate a PRS using PRSice-2. However, the issue I am having is that I do not have a covariate…

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[main_samview] fail to read the header

Samtools – [main_samview] fail to read the header 1 Hi everyone, I’m attempting to convert a SAM file to a BAM file using the following command: samtools view -S -b test.sam > test.bam However, I’m getting the error [main_samview] fail to read the header (see figure). The figure attached shows…

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bamdst gives error “EOF marker is absent. The input is probably truncated.”

bamdst gives error “EOF marker is absent. The input is probably truncated.” 0 I created a set of bam files from Poolseq data using bwa -aln, and all of the output files gave the following error when I ran bamdst to get summary statistics on read depth: “EOF marker is…

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Error in merged bam files

Error in merged bam files 0 Hello I am trying to merge unmapped and mapped bam files. I merged the bam files using the picard tool (gatk.broadinstitute.org/hc/en-us/articles/360036883871-MergeBamAlignment-Picard). I checked the merged bam using ValidateSamFile command (gatk.broadinstitute.org/hc/en-us/articles/360036854731-ValidateSamFile-Picard-) and it showed the below errors: Error Type Count ERROR:MATES_ARE_SAME_END 5496 ERROR:MISMATCH_FLAG_MATE_NEG_STRAND 5478 ERROR:MISMATCH_MATE_CIGAR_STRING…

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USU Software : 5 Mistakes to Avoid When Implementing Software Asset Management Tools

Thinking about launching a SAM program or purchasing a new SAM tool? Learn how to avoid the top 5 common mistakes that buyers encounter when implementing a SAM tool. Software Asset Management was introduced to me many years ago when a dear…

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Top Limitations of SAM Tools Guide

There is a common misconception that Software Asset Management (SAM) tools can completely mitigate your risk of a costly and disruptive audit. In fact, studies show zero correlation between having a SAM tool in place and whether you will end up paying audit fees or how much you will ultimately…

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Validation in new sample

Validation in new sample 0 Hi Sam, I am trying to validate in a new sample a PRS I conceived by PRSice. I would like to ask if using snp_prs function (bigsnpr package in R) is a good way for that or should I use another tool or method. Best…

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Segemehl -D option doesnt work for allowing differences

Segemehl -D option doesnt work for allowing differences 0 I am trying to map short some specific short reads (19~20nts) against long reads of a fasta file (F1.fasta). I used Segemehl tool and indexed the F1.fasta file (long reads) and then used the command line below to perform the alignment:…

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samtools mpileup fail to create bcf

samtools mpileup fail to create bcf 1 I have indexed my reference.fasta using bowtie2: bowtie2-build reference.fasta reference.fasta created the bam file form the sam file using samtools, sorted and indexed the bam file: samtools view -S -b Sample1_mapped.sam > Sample1_mapped.bam samtools sort Sample1_mapped.bam -o Sample1_sorted > Sample1_sorted.bam samtools index Sample1_sorted.bam…

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Whole Genome Sequencing via Pacific Biosciences (PacBio) Sequel DNA Sequencing Systems – 12305B21Q0093, West virginia

This is a combined synopsis/solicitation for commercial items prepared in accordance with the format in subpart 12.6, as supplemented with additional information included in this notice. This announcement constitutes the only solicitation; proposals are being requested and a written solicitation will not be issued.                 (ii) The solicitation number and a…

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How to build and run a docker container with multiple conda envs – General Discussions

As a novice to this community (and technology) I have only a basic knowledge regarding how to build and deploy a docker so i was hoping someone could provide some help. The situation is the following: I wanna create a docker container with two conda environments and I wanna call…

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How to extract all sequences mapped to a transcript from Kallisto output

How to extract all sequences mapped to a transcript from Kallisto output 0 I ran Kallisto with the –pseudobam option. How do I extract all the short reads that are mapped to a single transcript (e.g. ENST00000367969.8)? As a person without any previous SAM/BAM experience, I tried the following things…

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Extracting exons and transcripts from gff3/gtf

I was just doing something similar about a week ago. You may be able to accomplish this using the GenomicFeatures R package. First load up the following in R: library(GenomicFeatures) library(GenomicRanges) library(rtracklayer) Then you will need to get the chromosome sizes file, which you can generate with directions from this…

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