Biostar

9,161 results • Page 10 of 184

Hi, I have two bam files corresponding to genomes of two related species A and B. Both bam files have been mapped to a common third reference...I want to call variants between A and B. Can someone suggest a workflow? Are there tools to compare bam files directly for indels, SNPs etc

NGS variant BAM

updated 9 months ago • Yogesh

I'm attempting to downsample a bam file I have to 10 Million reads using seqtk. For example: seqtk sample -s100 myfile.bam 10000000 > myfile_10m.bam However...when I run this, there are 0 lines in my bam file. This doesn't seem to be correct. I'm curious if there is another way to downsample a BAM file to 10 Million reads

bam

updated 3.6 years ago • kstangline

Hi, I have a bam files produced from mapping by LifeScope Tool (mapping of SOLiD reads). I would like to know the length of the reads that...Hi, I have a bam files produced from mapping by LifeScope Tool (mapping of SOLiD reads). I would like to know the length of the reads that were...mapped to the reference genome based on the information present in bam files. Is there a tool which can give m…

bam mapping

updated 4.0 years ago • Jordan

Hello friends, I have multiple BAM files in my server, each of them is 9GB file. When I am trying to copy them to the hard disk, the copied BAM file has only 4GB. I tried...multiple times, what could be the issue? When I opened the BAM file, I could see alignment only till chr8

BAM Alignment DNASeq

updated 8.0 years ago • bioinforesearchquestions

Faster BAM Sorting with SAMtools and RocksDB http://devblog.dnanexus.com/faster-bam-sorting-with-samtools-and-rocksdb/ > We’ve been...hacking on a fork of samtools providing a new command, `samtools rocksort`, capable of sorting large BAMs significantly faster than `samtools sort` on modern server hardware. It leverages the flexible external sorting and

bam sam samtools

updated 2.1 years ago • Chris Miller

I get this warning when running cufflinks on my RNA-seq. Does not prevent me from doing my analysis, I' am just curious what it is. In short, I have paired end RNA-seq mapped with STAR (v2.4.1d) against GRCm38. ``` STAR \ --outSAMtype BAM SortedByCoordinate \ --runThreadN 8 \ --outSAMstrandField intronMotif \ --genomeDir ./GRCm38/star \ --readFilesIn [fastqfiles] \ --readFilesCommand…

RNA-Seq

updated 2.5 years ago • murphy.charlesj

Hi all, I want to write a bash script that reads in a BAM file and performs several processing steps with that input file. Can you recommend some ideas to write such a script? I...Hi all, I want to write a bash script that reads in a BAM file and performs several processing steps with that input file. Can you recommend some ideas to write such a script? I am...beginner and would be very happy…

Script BAM

updated 6.1 years ago • Jonas.Koch

I was given some bam files I used to call somatic variants. The high number of SNP and mutations i found seemed suspicious, so I asked for the...I was given some bam files I used to call somatic variants. The high number of SNP and mutations i found seemed suspicious, so I asked for the original...fastq files to redo the allignment. While waiting for them I tried to get fastq from those bam files…

bam bwa

updated 6.2 years ago • gab

Dear all, I have a question about analyzing BAM files with R. In BAM file, it includes all the reads. Are the reads already mapped to the reference genome? Eg, I want to find how...many reads in the BAM are mapped to a reference genome. I used the readBamGappedAlignments to get the reads. And it shows a number of GappedAlignments

r bam alignment

updated 11.4 years ago • shl198

Hi All, I am working with a BAM file generated using cell ranger. I am trying to edit the BAM file where i want the cell barcode and UMI to be added to the read...in CB tag. Similarly, for UMI, UR is UMI and UB is error corrected. I am using pysam to to edit the BAM file. bamfile = pysam.AlignmentFile("sample.bam", "rb") for read in bamfile.fetch('chr1',100,1000): if read.has_tag(…

alignment

updated 4.9 years ago • sam

Hi, I have this read in my BAM file. It maps on chromosome I. I open this BAM file in IGV, and I can see the alignment on chromosome I. But when I open this file...Hi, I have this read in my BAM file. It maps on chromosome I. I open this BAM file in IGV, and I can see the alignment on chromosome I. But when I open this file in R with Rsamtools: bamContigsCel <- Rsamtools::scanBa…

igv rsamtools samtools bam reads

updated 7.7 years ago • cristian

sequenced reads to the sheep reference genome. After that with samtools I converted the sam file to bam file. I'm interested for the reads that are aligned in the mitochondria, so I extracted the particular region from the bam...fie. So far everything seems ok, except the fact that the new bam file has "invalid BAM binary header". How can I keep the header to the new bam file? Thank you very mu…

sam mitochondria reference assembly bam

updated 3.1 years ago • vasilislenis

Hello I've downloaded a BAM file from UCSC and trying to familiarise with a few packages found in R. I'm currently using "Rsamtools" to import the BAM file

ChIP-Seq

updated 3.1 years ago • Constantine

Hello, HISAT2 can only output sam files, which can be quite large. I found an option to output only reads that mapped to the reference but still the files can be 100s of GB. Is there any issue in directly converting to bam as such: ${hisat2}/hisat2 -p 4 --rg-id=${4} -x $l --dta ${strand} --no-unal -1 $2 -2 $3 -U $4 | samtools view -Sbh > hisat2_output.bam I am specifically asking..…

RNA-Seq samtools

updated 5.9 years ago • Adrian Pelin

What does it mean "WXS aligned BAM file

wxs bam

updated 3.3 years ago • tea.vuki

Hi all, My Bam Files Size is (33,831,754 kb), after sort Its size (24,478,862 kb). I want to know that it's right? Thanks Mostafa

SNP

updated 7.1 years ago • mostafarafiepour

From My RNAseq data I have bam file. I need to extract the sequence of one of the genes from the bam file and look for the repeat regions. How can I do it

RNAseq

updated 2.8 years ago • Emili

I have about 20,000 bam files in a directory called intermediate_bams These will all have the same @HD and @SQ lines. There are about 860 @SQ lines...When I try to merge these bams, I get the following output: samtools merge -h custom_header.sam -o test.bam intermediate_bams/*bam [E::bam_hdr_write] Header...too long for BAM format Here is the header and tail of my custom_header.sam …

samtools alignments

updated 8 months ago • selplat21

Hi I have `BAM` files for tumour and matched normal for my samples from WGS. By uploading `BAM` files in `IGV`, how I could know how many `Variable

VNTR IGV WGS BAM

updated 20 months ago • fi1d18

I have a .BAM file that I have sorted using SAMTools sort command. Now I have to calculate the mapping statistics. I need to know how many...total reads are in the BAM file (both mates) and what percentage of the reads are mapped singletons. What command should I use

samtools

updated 12.0 years ago • komal.rathi

Hi, I'm looking for BAM files and their GTF files to test the featureCounts program. I would like these files in the mm10 genome (Mus Musculus) and...if it's possible not a too big file but smaller BAM files. Where can I found this ?? Thank you in advance

sequencing

updated 8.0 years ago • anais1396

the read group of every read and in the header. I would strongly prefer to not have to split the bam and redo everything with AddReplaceReadGroups. My question is: how can I add a tag (say "_T") to every RG ID in a bam, both in the

bam read-group

updated 7.2 years ago • danny

terms of indels (one group has the indels, the other doesn't). I already Mapped them and generated bam files. So, now I am struggling to get any form of usable VCF for my purposes. I am a little bit used to FST analysis of PoolSeq...module load BCFtools/1.3.1 module load SAMtools/1.3.1 # List all BAM files in current directory bam_files=$(ls *.bam | tr '\n' ' ') # Create…

Mpileup Samtools BAM bcftools VCF

updated 2.0 years ago • Human

360037224932?page=1#comment_4406762304155), it is ideal to submit the query name based sorted bam files, so will it be computationally intensive process to submit the coordinated based sorted bam files? First, I sorted...the unmapped and mapped bam files by queryname and merged these files and then sorted by coordinates. Can these merged bam files which are sorted by

Spark duplicates Mark

updated 3.6 years ago • priya.bmg

Hi all! Whilst fiddling around with the BAM format, I was a little surprised to see that since it supports the IUPAC codes when encoding DNA in 4-bits-per-base, and the...IUPAC only supports **T** *OR* **U**, but not both, that seems to mean that DNA in a BAM file can only have **T**; with **U** getting mapped to **N**. This got me thinking: - How do we currently store DNA-RNA hybrid fragment…

BAM SAM

updated 24 months ago • John

I use picard tools to take a BWA alignment sam file and convert it into a sorted bam file. Normally this works well, but for a small number of samples, I am getting VERY small bam files. e.g. SAM file = 42G, BAM file...831M Samtools produces the same BAM file size. If I take the bam and convert it back to SAM, the 42G file is reproduced. I'm confused as to why the BAM file is so small...when fo…

sam bam picard

updated 11.1 years ago • Clare

I get an error while uploading BAM file. I used bowtie to map small-RNA reads against one mRNA fasta file. I sorted and indexed the bam file but I get the error...I get an error while uploading BAM file. I used bowtie to map small-RNA reads against one mRNA fasta file. I sorted and indexed the bam file but I get the error in uploading it on IGV: ```Error loading BAM file: htsjdk.samtools.SAMExce…

software error igv bam

updated 4.5 years ago • Apex92

How can I convert BAM data directly to GENOMEDATA ? I guess I could convert BAM data to FASTA data and then FASTA data to GENOMEDATA but I'm afraid...https://hoffmanlab.org/proj/genomedata/) files as its input. The files I'm trying to process are BAM (https://samtools.github.io/hts-specs/SAMv1.pdf) ones so I need to convert them before I can use SEGWAY.] Thanks, Armand

BAM genomedata

updated 2.0 years ago • Armand

Hi, I have a paired-end BAM file and I found that some pairs/mates have identical positions on the chromosome, i.e., the numbers in the POS and PNEXT...Hi, I have a paired-end BAM file and I found that some pairs/mates have identical positions on the chromosome, i.e., the numbers in the POS and PNEXT fields...same. I want to remove these reads. I also found that some reads present more than 2 …

next-gen

updated 2.7 years ago • lisadavic66

from 1000 genomes project. In order to see if there is a deletion of interest. I have downloaded bam file and extracted a region of interest using samtools. I believe reads in bam file are already aligned. How do I assemble...it says in the description that it is for very short reads. Are there any alternatives which take bam files? Is velvet a good tool for my task

1000 genomes Assembly alignment primer

updated 10.4 years ago • eyb

I am on paleogenomic data. I have BAM files from two different datasets that were processed/sequenced different (one was partially UDG treated, one was not...effects. One idea my adviser asked me to try is clip the first 5-10 bp off all reads within all BAM files. The problem is neither of us know how to do that. Anyone here know of a way to trim reads within a BAM file

bam

updated 5.4 years ago • devenvyas

Dear all, I am trying to write a fastq file (to be more exact a fastq sanger) from a bam file. I tried to install bam2fastq (https://github.com/jts/bam2fastq) but I seem to be unable to install it correctly (which...Dear all, I am trying to write a fastq file (to be more exact a fastq sanger) from a bam file. I tried to install bam2fastq (https://github.com/jts/bam2fastq) but I seem to be u…

command line sequencing

updated 8.3 years ago • michaela_boell

in finding CNV's for my sample. I aligned the reads with ref genome using bwa mem and obtained bam file. I looked at Varscan for CNV's but it requires 2 bam files ; normal/ref and sample. Is there a tool which can find CNV's on only...single bam file? My reference genome is yeast Hope to hear from you Regards Varun

cnv

updated 3.2 years ago • Varun Gupta

Hi there, How to find/filter intron-retained reads from BAM files? Which flag in BAM file describes information about retained intron. I know there are some tools to find retained...intron, but i want to understand how they are represented in BAM files. When there is an intron retention, portion of reads map to exon and remaining to intron. Is this correct? thanks

samtools intron-retention

updated 7.0 years ago • Chirag Nepal

Hello! I have a BAM file that was aligned to Feb. 2009 GRCh37/hg19 Assembly, and I would like to convert it to a CRAM file. I use this command: samtools...reference for id 0 [main_samview] failed to write the SAM header Also, I know that my BAM file is sorted as the header returns -> SO:coordinate What do you think can be the issue here

samtools cram bam

updated 3.7 years ago • nrk_02

Hi, I am trying to merge two different bam files with Rsamtools in Rstudio. And this is how I am trying to do it: mergeBam(files = files[c(3,5)], destination = "O:/ChIPseq_results_files...bam_files/merged_bam_files") where files is the list of bam files I have in a given directory and 3 and 5 the files I am trying to merge (that is why I write `files[c(3,5)]`). However, I am getting

mergeBam Rsamtools

updated 3.9 years ago • rbravos87

Hello everyone! I am trying to rewrite an existing bam file via pysam. I have reference.fasta file and file_to_be_changed.bam. I would like to change the nucleotide on a read...of the nucleotide and the reference position. For example: pos 0123456 ref ATCGGTC bam ATCG CGT GGTC I think that the problem could be solved with: if pos_on_read ==…

pysam rewrite bam

updated 3.1 years ago • Anst

I have some genomes assamblies (BAM file) from Illumina sequencing. I would like to evaluate sinteny breaks in the chromosome 1. However, I have found software...would to know how could I make similar analysis or how could be the correct pipeline to transform my bam files to fasta and then make the analysis. Thanks in advance

assembly genome gene sequence

updated 4.4 years ago • Lissa Cruz Saavedra

Hi everyone I have dna seq dataset for S.cerevisiae genome. I have aligned bam files and the ref seq genome. I would like to know some methods for finding snps from the bam files as input. I know 2 ways to

snps

updated 11.8 years ago • Varun Gupta

Hi I am getting a message while converting sam to bam. I used this comand for mapping: bwa mem -M -R '@RG\tID:sample1' -t 2 ref.fa sample1_R1.fastq sample1_R2.fastq > sample1.sam...Now I tried to convert sam to bam, using: samtools view -hSb PI200492.sam > PI200492.bam and I got an Error [W::sam_read1] parse error at line 1 [main_samview

genome

updated 7.5 years ago • valopes

Does anyone know if it is possible to convert Eland file to BAM

next-gen sequencing bam

updated 14.2 years ago • Zack

pipeline run faster. Right now we're settled on aligner, but everything to get us from the SAM/BAM creation up to a sorted, merged, duplicate marked BAM could be updated. We'll need tools to help us: - Sort - merge - mark duplicates...flagstats - make bam indices (.bai) On my list of tools to evaluate, I have some combination of the following: - samtools - picard - sambamba - samblast…

sam markduplicates sort bam

updated 2.9 years ago • Richard

Dear all, I am trying to separate mapped and unmapped reads from a BAM file following [these instructions][1]. But when I run $ samtools sort .bam -o .bam $ samtools view -F 4 .bam > _mapped.bam then I get...Dear all, I am trying to separate mapped and unmapped reads from a BAM file following [these instructions][1]. But when I run $ samtools sort .bam -o .bam $ samt…

sequencing sequence Assembly

updated 6.7 years ago • marongiu.luigi

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...biological replicates), however I have a lot of group variability. I'm thinking to merge all this 5 bam (I know that is a dirty things) in order to make a unique bam file (already done using samtools merge) and then split (in a random...way) in 5 new …

samtools

updated 21 months ago • g.persic1991

of the samples, I had the original fastq files. For a couple of my samples, I was only given a bam file. So what I did was use Picards "SamToFastq" function to convert the bam file back to a fastq file. Since I didn't know how...with Picard. I then used samstool for variant calling. All of the samples that were originally bam files, weren't get any of their variants called when I looked at the …

assembly alignment genome next-gen

updated 6.8 years ago • williamsbrian5064

Dear Colleagues, Is there a way to filter out reads with specific properties from bam file, for example, after mapping my small RNA reads to a reference genome by Bowtie, I would like to filter out all the mapped...reads that have a stretch of 3 G bases ("GGG") at the beginning of the reads from the bam file and I would like to have two output bam files in which one bam file having all the read…

RNA-Seq CLIP-seq

updated 5.1 years ago • xiaoleiusc

How to use Ruby BioSamtools for SNP finding on .bam and .sam files? Does my code call variants or not, I am not sure... ``` #!/usr/bin/ruby # making script executable require 'bio-samtools...calling rubygem bam=Bio::DB::Sam.new(:bam=>"my.bam",:fasta=>'fake.fa') # creating bam object bam.open bam.index bam.mpileup do |pileup| # calling variants...how to call them on a bam or sam …

ruby bioruby samtools

updated 2.7 years ago • elvissober

Hi, I would like to know if there is a way to isolate discordant read pairs from a bam file. For example, when I use samtools stats in my bams, I can see the number of outward oriented read pairs and I would like

samtools NGS

updated 18 months ago • paulaotero.sanchez

Given a BAM file that is only computer readable how can I check if it comes from a illumina machine? I tried doing grep -q "ILLUMINA" filename.sorted.bam...To check if ILLUMINA word appeared but it did not appear, probably due to the fact that BAM are not human readable therefore word does not appear

BAM ILLUMINA

updated 20 months ago • Manuel Sérgio

I would like to make a minimal example of my wgs .bam and .bam.bai files to accelerate pipeline testing. For example, i would like to select chr1:1-1e7 & chr1:1-1e7 regions and...create that same .bam .bai file from them. How to accomplish that

bam

updated 3.3 years ago • optimistsso4co3

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