Biostar

9,147 results • Page 6 of 183

Hi, I need to download BAM files regarding a study from CGHub data base (https://browser.cghub.ucsc.edu/). For some samples, there are two types of BAM

bam

updated 11.1 years ago • sarahmanderni

LN:42210 @SQ SN:NT_187367.1 LN:176043 @SQ SN:NT_187368.1 LN:40745 my tired converting to BAM result file looks like this BAM?U�:^@HD VN:1.0 SO:unsorted @SQ SN:NC_000001.11 LN:248956422 @SQ SN:NT_187361.1 LN:175055 @SQ SN...SQ SN:NT_187366.1 LN:42210 @SQ SN:NT_187367.1 LN:176043 @SQ SN:NT_187368.1 LN:40745 my bam file siz is more than 5 gb i want to sort it b…

next-gen sequencing rna-seq

updated 7.9 years ago • sa1987

I read about this BAM edit in this page: https://useast.ensembl.org/info/docs/tools/vep/script/vep_other.html section Correcting transcript...models with BAM files. What I don't understand is, how VEP actually correct this? For example, this transcript NM_030582.4 has BAM edit which

variant VEP

updated 8 months ago • bharata1803

I am interested in retrieving sequencing barcodes (demultiplexing barcode, not UMI) from sorted BAMs. I thought that I could first convert BAM > FASTQ and look in the header (bedtools bamToFastq), but I don't see an index sequence...below). I am hoping that I can extract this information directly from the BAM. Any help would be appreciated! @NS500602:778:HHH5KBGXB:4:11605:4703:18870 GGC…

BAM FASTQ Index

updated 5.1 years ago • trodriguez2011

Hi, I have many BAM and BED files. I am looking some novel transcripts (missed) from my BAM file. Is there any way to extract new transcripts from...my BAM file. any suggestion

next-gen alignment RNA-Seq

updated 6.8 years ago • barrypraveen

Hi Biostars, I have multiple murine whole genome sequencing samples which show a non-uniform readcount distribution along the genome, all following the same pattern, example attached. Has anyone be facing this pattern...in readcount distribution before and may have an idea what could be causative? (i dont see patterns in standard QC parameters...bias: GC content was proposed as a reason, so I…

WGS fluctuating coverage

updated 3 months ago • BioStar22

I have RNAseq data and aligned the fastq files to the genome. so now I have bam file. I want to make the bam file only for one gene for example gapdh. to do so at first I have converted the bam file to sam file...the coordinates of gapdh I did not find them in the sam file. do you know how I can make a sam or bam file only for the gapdh

rna-seq

updated 6.7 years ago • alireza346

How can I convert a bam file to a wig fixedStep of step=1? I found this answer, but it creates a variableStep instead of a fixedStep: http://biostar.stackexchange.com...questions/10592/convert-bam-to-wig

samtools bam wiggle

updated 13.2 years ago • 2184687-1231-83-

Hi, Having two BAM files from NGS data, how can one check if they are the BAM files (left and right) from a paired end mapping of the same sample

paired-end bam

updated 9.1 years ago • sarahmanderni

Hi, I am trying to calculate the sequencing depth for `sorted bam` files made using `bowtie`. I am using: samtools depth bowtie_sorted.bam | awk '{sum+=$3} END { print "Average = ",sum/NR}' I have many `sorted...bam` files and I want to calculate the `depth` for all using one `array` job rather than calculating for all files individually

next-gen

updated 5.7 years ago • evelyn

I am back again with one more naive question. What according to you is the best way to Normalise a BAM file (read density) and why it is the best available method? Kindly, name the tool(s) you use to normalise the BAM files. More Details

chip-seq

updated 11.4 years ago • ChIP

of the transcript. After i map my reads to this reference, i would like to visualize the resulting bam file in IGV. For that to happen, i would probably need to convert the coordinates in the bam file to the hg38 coordinate system...which is given in the id of each transcript). What would be the best approach to change the bam file? Bam -> Bed + convert coordinates -> Bam? Or is …

bam RNA-Seq

updated 7.4 years ago • Gregor Rot

Hello. I want to use Tablet to visualise the aligned reuslt(bam format).All the data were download to my laptop before run tablet. When I input the files(.bam and fasta reference)into Tablet...It shows that a index file needed for it. So I used "samtools index .bam" to create a index file and download it into the samefolder in my laptop. When input it again. it shows that one of the files

updated 13.8 years ago • Haiping

Is there any tool to convert BAM files that have been produced against Ensembl genome references to UCSC-compatible BAM files? And viceversa? AFAICS, Ensembl...names don't have the 'chr' in front of the sequence name, but UCSC does, so when I try to attach my BAM file to UCSC, I get this error: Error Unrecognized format line 1 of ftp://somewhere.com/pub/myfile.Mus_musculus.NCBIM37.61.bam

bam ucsc ensembl reference

updated 7.8 years ago • 2184687-1231-83-

alignments in IGV. Is there any tool similar to IGV that would allow looking at a small window in a bam file, manually moving some of the difficult to align reads in that region -- this is, changing the read alignments, then saving...that window of the bam as another small bam file? The only way I can think of right now is to export the bam window to multi-fasta, open it with Jalview...edit the …

bam alignment

updated 10.7 years ago • 14134125465346445

I have a list of values for a bam tag called XC (say needed.txt). I would like to extract the alignments which have these values from a bam file (say bamfile.bam

alignment

updated 7.1 years ago • sumithrasank75

zzz_02.bam ${path_to_strelka}/bin/configureStrelkaGermlineWorkflow.py \ --bam xxx_00.bam \ --bam yyy_01.bam \ --bam zzz_02 \ --referenceFasta \ --callRegions <.bed.gz> \ --runDir # execute strelka2 ${dir}/runWorkflow.py...file ovverwrites the other and I only get 1 genome file in results/variants. for bam_file in *.bam ; do …

strelka2

updated 5.3 years ago • bioguy24

Hi everybody, I have found an old description of how to convert a bam file into wig using perl. ([How can I convert BAM/SAM to wiggle][1]). In this example (as far as I understood it) the whole bam file was...but somehow it doesn't work. I keep getting this error massage: [bam_header_read] invalid BAM binary header (this is not a BAM file). Does anyone has an idea how to run this comman…

bam conversion wiggle samtools

updated 2.7 years ago • Assa Yeroslaviz

to infer tumor purity and ploidy, but I have a question for the input. Can ABSOLUTE work for WGS bams? If not, how can I convert the bam to the input needed by ABSOLUTE? http://www.broadinstitute.org/cancer/cga/absolute_run

tumor

updated 2.6 years ago • lyz10302012

Hello! I was wondering about the consequences of converting BAM files to FastQ (maybe with bedtools or samtools). Is there any significant downside of using the FastQ files that are obtained...by converting BAMs to FastQ? Thanks

fastq bedtools samtools bam

updated 3.7 years ago • nrk_02

I'm working with some RNA-seq data. I have alignments done in STAR and the resultant BAM file. I'd like to annotate this BAM alignment data with custom tags using data that are stored in a separate file. The data...contain are a read ID, a barcode, and a UMI. I want to add the barcode and UMI to all reads in the BAM file that match the read ID in the second file. To summarise: First file: BAM o…

alignment RNA-Seq sequencing BAM SAM

updated 7.7 years ago • dzb

Hi, I'm trying to use bwa mem for the first time and I wonder, is it possible to run it on a bam file instead of a fastq file? I noticed that bwa aln can be runned on bam file using '-b' but this option is invalid for bwa mem...The manual does not mention whether it is possible or not. I tried to simply run bwa mem on bam file and the output seems to be a header only sam file. Does anyone has e…

NGS bwa-mem bam

updated 2.8 years ago • vimartin

Heys, I'm trying to run GATK on some BAM files I got. When I try, I obtain this error message: > A USER ERROR has occurred: Argument emit-ref-confidence has a bad value...Heys, I'm trying to run GATK on some BAM files I got. When I try, I obtain this error message: > A USER ERROR has occurred: Argument emit-ref-confidence has a bad value: Can only be used in single sample mode c…

bam snp calling samtools

updated 4.2 years ago • gubrins

I want to do remove certain reads from my bam file and the output is quite funny .. I tried trim out BAM files with samtools view and awk, but the size of the output BAM files...is tripled. Thus, if I re-use this output bam file it says that the header is missing. For example when I do the following : samtools view 10iPS-1.sorted.bam | awk ' BEGIN...gt; 1IPS-BAM1-RQ.bam I don't think that A…

samtools bam

updated 12.7 years ago • madkitty

set of files generated by ion torrent server. It seems that the server produces a fastq file in the BAM format. I am quite surprised because I have been using an Illumina dataset, which produces a fastq file. The BAM of PGM looks...quite different in comparison to the Illumina bam file(samtools view -H ion.bam), Any suggestions how to generate a Fastq from this bam. Thank you

sequence Assembly genome Ion torrent PGM

updated 9.9 years ago • alok.helix

softwares like bam2fastq. However, in order to speed up, I tried to split the large bam files (sorted according to coordinate but not read name) chromosome by chromosome, and would extract based on each bam file...read paires which map to different chromosomes. So I'm just confused any optimized way to split bam files first and then extract for each of bam, so that to improve speed? thx Edit: I…

fastq

updated 12.9 years ago • michealsmith

Hi bioinformaticians, I run STAR with this command but I don't see the Bam file output, just a Sam file in the home directory. Would anyone please tell me why? Thank you so much! STAR --runThreadN 8 \ --runMode...doan/hg38/hg38_index \ --readFilesIn /home/doan/data/demo_trimmed.fastq \ --outSAMtype BAM Unsorted Update. The size of this sam file is 0

STAR

updated 2.6 years ago • Chris

dual RNAseq. I have my transcript aligned to human genome and the resulting Sam file converted to bam file. I’m using samtools version 0.1.19. Now I want to sort the bam file and each time I run the program using the command: (samtools

RNA-Seq samtools

updated 6.0 years ago • Liftedkris

Hello! Is there any way of changing all variants, which are listed in vcf file, in bam file? If there are several alleles, we take random one from them and place one the position in bam file. Thanks

vcf samtools bam pysam

updated 21 months ago • Anst

hi friends I have a bam files and I can want to view it into ucsc browser, I have to just upload into custom track option or edit it by custom track...line and what is meant by bam and bai files

ChIP-Seq

updated 2.3 years ago • Azhar

I wanted to merge two BAM (alignements) files together. Before merging, how can I color the reads in the BAM files so that while viewing at the UCSC Genome

bowtie bam alignment

updated 11.1 years ago • troym2026

Hi, I have some bam files and I want to convert them to bam.bai files. I am very new to programming and have used some R Bioconductor packages...I was wondering whats the code for using Rsamtools to index the bam files. Thanks

next-gen

updated 8.9 years ago • jain.harshika

So I have a full genome PACbio BAM file and this has a average coverage of 3-6. Now I want to split the bam file per read. Since readgroup is not working and sometimes...still gives me multiple reads inside my BAM. The reason why I want this is because i want to run MPILEUP with only 1 read per bam, so that I can identify insertions/deletions

BAM manipulation

updated 4.0 years ago • s.vdrzeeuw

Hi, Wondering about the validity of converting bed to BAM, for instance in terms of TF foot printing...if lets say Ive done some analysis and gotten a consensus peak set in BED format...well after Macs2 peak calling, and I want to convert that to a BAM file for foot printing would this be a valid thing to do? How does that conversion represent or misrepresent read depth...in the newly made BAM f…

ChIP-Seq sequencing BAM bed footprinting

updated 7.4 years ago • rbronste

and in its pages, [RealignerTargetCreator][1]. It states that it takes multiple inputs as Bam. But its not taking it. when I checked Galaxy.it stated that GenomeAnalysisTK: RealignerTargetCreator accepts **an** aligned...BAM input file. I want to give all my Bam files for indel realigner intervals. Here's the command that I am using; java -jar GenomeAnalysisTK.jar

GatK RealignerTargetCreator Bam

updated 7.8 years ago • micro32uvas

Hello all, I am new to NGS analysis and still learning things. Currently i am trying to get bam files metrics. i used the gatk CollectAlignmentSummaryMetrics command. but i didnt get all information i need . preferably...the following metrics. Total reads in bam file total reads passing mapping quality filter total reads mapping to multiple genomic locations total reads in cov…

ngs bam gatk

updated 3.9 years ago • Sabeen

Hello, I'm working with paired end rna-seq data so two fastq files produced 1 BAM file. I know col 10 represent the seq and col 11 have its ascii code for quality. If the original seq length 100bp when I extracted...some seq from BAM file I noticed some reads of length LESS than the original length. For example in one location one seq has cigar (40M, which...Another point, in this case we have p…

RNA-Seq next-gen alignment

updated 6.8 years ago • Lolla

Hi, I'm looking for a method/tool for annotating a bam file. After running the mapping with STAR, I have filtered my bam file for specific reads, I am interested in. I would now like

bam annotations

updated 4.3 years ago • Assa Yeroslaviz

The GATK often requires that the BAM contains some extra informations in the header ( Group ID, Group Library, SO:coordinate...). Which commands I should invoke...The GATK often requires that the BAM contains some extra informations in the header ( Group ID, Group Library, SO:coordinate...). Which commands I should invoke after...bwa so my SAM/BAM files (1 sample/file) are valid for the GATK ? …

gatk sam bam

updated 13.0 years ago • Pierre Lindenbaum

Given BAM file and its BAI file, how can I calculate the TMB for the patient? This bam file is the result of target sequencing, so I would

BAM GATK TMB

updated 20 months ago • Manuel Sérgio

I would like to change some information in the BAM header (specifically, chromosome size information). Is there a smarter/faster way to do this without extracting to an intermediate...SAM file and remaking the BAM file from the edited SAM file

bam

updated 22 months ago • Alex Reynolds

Hi everyone, I am just trying to create a bam file that contains only intergenic regions of genome. I have complete genome bam file but i couldn't find out any filtering

R genome intergenic alignment

updated 8.6 years ago • erincyurtman

Dear all, I have a .fa file for my organism and several .bam files for my isolates. I have designed some PCR primers for the isolates. Are there any programs that would allow me to run...In silico PCR with the bam files? Thank you

PCR BAM

updated 8.4 years ago • zaroteary

I have a TopHat large BAM file of 10GB and when I do Cufflinks with this 10GB file it takes too much time and eventually it hangs. Is it possible to...I have a TopHat large BAM file of 10GB and when I do Cufflinks with this 10GB file it takes too much time and eventually it hangs. Is it possible to split...this file chromosome-wise and with smaller BAM file Cufflinks is done

RNA-Seq

updated 7.5 years ago • qudrat

I've a BAM that I'd like to show its coverage off in [a circos plot](http://circos.ca/documentation/tutorials/2d_tracks/histograms...I've a BAM that I'd like to show its coverage off in [a circos plot](http://circos.ca/documentation/tutorials/2d_tracks/histograms/images...Is there a standardised way of going from a BAM file towards such a histogram in circos

bam

updated 4.0 years ago • Sander Timmer

with GATK to do the SNP calling of some target capture sequencing data. Right now I'm creating the bam files and I was wondering which are the standard quality measures I should apply to my bam files. I'm aware that I can mark...or they are just marked and I have to do something else? Should I specify some value scores for my bam files? Thank you very much for your help

gatk bam sam quality

updated 4.8 years ago • gubrins

mitochondrial in this case), and due to the aDNA's nature, the final assembly has gaps in it. I have BAM files and I want to convert them to FASTA, so I used samtools fasta command for it, but then I got multiple FASTA's per a single...BAM, one FASTA one for one covered region in the same mtGenome. But I want to make a single FASTA file for each BAM, where the uncovered

genome sequence next-gen

updated 7.8 years ago • gerberd1990

Dear all, I have an already aligned .bam file stored in google bucket. I'm trying to retrieve and ummap them to ubam so i will be able to perform all analysis using...When i use gsutil cp gs:url/to/file/in/google/bucket there's an additional .gstmp extension at .bam files from google bucket. Samtool view tells me that EOF marker is absent; is this a problem with downloading my .bam files...f…

next-gen alignment google-bucket

updated 5.4 years ago • ekwame

Hi, For the purpose of an experiment on a panel of amplicons, I have to work on bam files that I have already filtered using samtools on the positions concerned by the amplicons(with a bed file), for a total...of 1840 bam files (10 bams x 184 amplicons). I need to replace the chromosome names by the amplicon names. I already have the lists of chromosomes...OLDNAMEFILE=name_to_be_replaced.txt …

samtools BAM

updated 21 months ago • ltalignani

None of my BAM files have a correct sample ID in their header, they all literally say "sample_ID" I didn't catch this until after SNP calling...How can I get the BAM headers to have the name of the sample that they are? I have over 2,000 BAM files

bam snp samtools

updated 5.6 years ago • marcus.hooker

9,147 results • Page 6 of 183

Recent Votes

Comment: GBWT Construction Error: "Sources X and Y both have node Z" When Building GBZ fr

Comment: Software for visualizing mass spectromety spectra

Comment: nanopore SNV callers returns empty VCF

Answer: GBWT Construction Error: "Sources X and Y both have node Z" When Building GBZ fr

Avoiding the Pitfalls of the Anaconda License: A Practical Guide

The Biostar Herald for Wednesday, March 19, 2025

How do I figure out pangenome location of hg38 coordinates?

Recent Locations • All