Biostar

9,145 results • Page 4 of 183

Hello all :) Is there anyway to check if a BAM file is complete and obeys all the BAM standards? I have created 100 processed BAMs from 100 unprocessed BAMs, and before...there are some things it would be impossible to know was wrong - like I might have mapped all these BAMs to the wrong genome, etc. I'm not looking for those sorts of errors. I'm mainly looking for truncated BAMs, or BAMs where…

BAM

updated 2.7 years ago • John

CNVkit to generate CNV calls. My question is, is it better to use base quality score re-calibrated bam file than original bam file

sequencing

updated 5.8 years ago • donglei.hu

If I have a .vcf file, how can I convert it to .bam file

vcf bam

updated 9.5 years ago • Madhuri Haque

I found one wired thing about Bam file. The size of my original Bam file is about 13GB. I converted the bam file into sam file and extracted the reads with mapping...than 10. I put these reads into a new mini sam file and converted this mini sam file into a mini Bam file. The size of the mini bam file is about 2.5GB. However, I actually plotted the histogram of the distribution of mapping...scor…

next-gen

updated 3.3 years ago • devinliao0918

Is it possible to unalign an aligned TMAP bam file? I am only sent the aligned bam but would like to use other aligners such as bowtie2 or bwa-mem to do additional QC. Can...I use a tool on the aligned bam to create fastq or am I better off getting the unaligned bam as well? Thank you

ngs

updated 9.5 years ago • bioguy24

I have five exomes(in bam format), each a different sample, that I would like to merge into one bam. None of the bam have @RG's in the headers, I am assuming...Picard documentation states you must pass in a value for UNMAPPED_BAM (definition Original SAM or BAM file of unmapped reads, which must be in queryname order. Required.) I don't undstand what this file is? When I did my alignment

picard samtools

updated 5.8 years ago • Tryingtogetthere

I'm trying to convert a BAM file to a BIGWIG file on my mac using the following link: https://github.com/chapmanb/bcbb/blo...m_to_wiggle.py Could someone...explain what commands I have to put into the terminal (or in Sublime Text)? My BAM file is called Galaxy6RmDupdata.bam. I couldn't figure this out myself from the explanation in the link itself. Any help

github bam bigwig terminal

updated 23 months ago • robbenstijn

chipseq for a transcription factor with two replicate in each experiment. I want to merge the bam file of replicates but I do not know what condition is required for merging bam file. Every replicate file has different...sequencing depth and their alignment is also not similar. What is exact condition when bam files can be merged? Any leads would be appreciated

Chip-Seq MACS2 bowtie2

updated 21 months ago • qudrat.nii

Hi all, Hope someone can help. I will be getting several BAM files from users and they may not inform us which reference file to use. Is there any way to look into a BAM file and know for...some way that I could infer which file to use. For e.g. I believe that 1000 Genomes uses their own bam file whereas Illumina used UCSC fasta files? Any ideas? Thanks, A

bam

updated 24 months ago • win

Hi guys, Any tools or software available for converting bedgraph to bed and then to bam? I would like to extract CpG methylation calls using bismark and then save them in Bam format then convert them to bam using

bed

updated 2.4 years ago • wanziyi89

Hi all, I wonder if there is any tool (in samtools ?) to quickly know whether a BAM file has been sorted or not. (longer story: I've merged a set of sorted bams using 'samtools merge' and I've then used MarkDuplicates...Pierre UPDATE: I wrote a post about it : http://plindenbaum.blogspot.com/2011/02/testing-if-bam-file-is-sorted-using.html

bam next-gen sequencing sort

updated 8.0 years ago • Pierre Lindenbaum

After completing genome mapping I have few bam files which I need to convert to count data. How should I convert the bam files to count data in r studio

Bam

updated 24 months ago • Rana01

I have up tp 1000 bam.files need to put in bedtools multicov -bams like bedtools multicov -bams 1.bam 2.bam .....1000.bam. how can i work it with shell code

software error Linux

updated 4.8 years ago • fuhaolll2

Hi, I have a question in converting bam to bed, while convert bam to bed and import them to IGV, you can see they are different. Only bam file can align well to refseq...exons. Does bedtools change the genome coordinates in bam files? image: http://postimage.org/image/68ynlxui3/ Thanks a lot

format seq

updated 12.5 years ago • camelbbs

I have BAM files in the external hard drive. Want to convert them into BED. Am using cd /media/usr/LaCie/work/client/pool1/bam for x in *.bam...do echo "print current:$x"; bedtools bamToBed -i "$x" > "${x%.bam}.bed"; done echo "done" it writes the BED files in the directory, but they are all empty. My BEDtools is installed in /home/usr/miniconda3...bi…

Bedtools shellscript BAMtoBED

updated 4.3 years ago • amitpande74

Hi ! I have many .bam that I want to get their .bai using samtools in the terminal. I tried the following command : samtools index *.bam However, I did

next-gen-sequencing samtools

updated 20 months ago • Kizuna

Hi All, Using this command line, I converted two Paired bam files: samtools fastq -1 ${sampleID}.sorted_1.fastq -2 ${sampleID}.sorted_2.fastq ${sampleID}.sorted.bam 1st File: Bam 8.4G Fastq1...8.1G and fastq2 8.1G were produced. Fastq1 494M and fastq2 494M were made by Bam 1.8G. Then I use the nf-core nextflow RNA seq pipeline in the cluster, which results in the following error: ``` E…

Fastq Bam

updated 21 months ago • وفاء

I have a list of sam files that were created using HISAT2. I need to convert all of them into bam files for downstream analysis and I do so using the following (so it runs on all sam files in the directory) samtools view...7 -b -S -o *.sam > *.bam the operation runs but nothing happens in the output files (I can't even see them). Ideally I would want a bam file being in the

rnaseq sam bam samtools

updated 8.3 years ago • V

I have two WGBS unaligned bam files (fastq files stored as unaligned bam). I am wondering can I merge those files? Does samtools merge works for unaligned...bams? Thanks

next-gen

updated 5.5 years ago • irfanwustl

Hi all. I am curious if there are any tools to quantitatively compare the similarity of two BAM files. There are many documented methods for comparing similarity between two or more fasta files: simple sequence distance...approaches, so much more. However, I am interestedin ways to put a number on similairty of entire BAM files. Obviously, I know there are many different ways of thinking about…

bam

updated 23 months ago • rafi.schulman

Dear All, This is my first post on this site.I have different bam file size of 10gb, 50gb, 200gb, ... 600gb. I want to split these .bam files into 1gb file each(for ex. 10gb .bam file split into 10 1gb...bam file) and later I want to insert into database all these chunks. I am using threading to insert these files, If I try to insert

genome split bam

updated 3.3 years ago • kavitarege

Hello I am downsampling BAMs down to 10% on control samples to check at what minimum read depth are we able to detect a certain set of SNPs. What approach...do people usually adopt for this 1) downsample the same BAM 3 times with different seed options and then take the average of the read depth ? sambamba view -h -f bam -t 10 --subsampling-seed...3 -s 0.1 $BAM -o $downsample_0.10.bam…

downsample targeted-NGS sambamba

updated 5.9 years ago • Nandini

Hi everyone, is there a way to introduce a specific artificial deletion in a bam file? I'm searching something that take a particular interval of coordinates and remove it from the bam file e.g. chrx:3122135

bam

updated 11 months ago • enee

Hi all, I want to extract bam of specific amplicon to evaluate the according amplicon performance. I used to use samtools view xx.bam chr:start-end...to extract the bam, however, if the two amplicon are totally overlapped, this command will return us the whole reads covering the two region...gt; <------------------- I firstly convert the bam to bed using bedtoo…

bam region

updated 7.3 years ago • J.F.Jiang

Hey Guys Just wondering if anyone there is now storing the raw fastq data as unaligned bam files. We are reaching a stage where any space we could potentially save would be beneficial. Any con of storing fastq as...bam? I see some discussion about this on seqanswers: http://seqanswers.com/forums/showthread.php?t=14941 Also any tools that...people already have that converts a fastq to bam and …

bam fastq

updated 2.6 years ago • Abhi

samtools view -S -f0x4 alnIRGSP.sam > UNMAP.sam. After that i could not convert this sam file to bam file . I get the below error. [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid...BAM binary header (this is not a BAM file). [main_samview] fail to read the header from "sortUNMAP.sam". Can anyone help me to solve

samtools

updated 8.6 years ago • sukesh1411

Hello. I produced BAM files which were produced from SAM files and sorted using the samtools. I want to open these files for checking and analyzing...results of mapping process. What programs are required for opening BAM files

BAM

updated 2.3 years ago • ongchip

Hello, Is it possible to get a gVCF from VCF file and a BAM file? I know I can get a gVCF from BAM file by using HaplotypeCaller for variant calling but my plan is to use a different tool

gVCF

updated 2.2 years ago • tejaswikoganti

Can anyone help me unalign BAM files that have been aligned using TMAP? I want to run my raw reads through GATK best practices but the BAM files we received

TMAP BAM IonTorrent

updated 10.0 years ago • M. Khan

Hello, I am new to sequencing analysis and ready to work on bams of tumor-normal pairs. I would like to know how to get the information of programs done on a bam file. Does @PG in header mean

SNP sequencing bam

updated 8.7 years ago • zhoub

30 pair end reads file separately to the genome. now please suggest how to merge these 30 mapped bam files to generate single bam file to do genome guided assembly

RNA-Seq

updated 8.0 years ago • Bioinfonext

The Bam format was developed at a time when I/O (disk / network) was not a limiting factor for genomics data analysis. Currently it...The Bam format was developed at a time when I/O (disk / network) was not a limiting factor for genomics data analysis. Currently it is...Especially when you have pipelines like GATK that process BAM files in multiple steps and read and write bam files for every ste…

cram bam io hdf

updated 3.9 years ago • WilliamS

Hi guys, I'm trying to run ChipQC with my bam files and narrowPeak files. But I have several different version of bam files with single dataset such as mapped bam, sorted...bam, markduplicated bam Which one should I use for chipQC? Thank you in advance

ChipQC Chip-seq Bam

updated 3.4 years ago • chansik

I have an indexed bam file. I wish to update the sample ID (SM) field in the read groups (RG) entries in the bam header, which I do using `samtools reheader...I was wondering if it is recommended to re-generate the bam index (.bai) file after editing the header. The bam index specifications do not mention read groups so I do not know if read

bam

updated 14 months ago • dolevrahat

Hi, I am trying to run Salmon on bam files generated by STAR. I am new to using Salmon. I know that I cannot run Salmon on bam files obtained by aligning to the genome...aligning to the genome is somewhat better than aligning to the transcriptome. Therefore, I generated bam files by aligning to the genome and outputting the alignments in transcriptome coordinates by setting --quantMode Transcrip…

salmon STAR collate

updated 4.4 years ago • inah

is related to the manufacture of snp database. constraints that occurs is how to read the file. bam. in this case, I want to take the data from the file. bam whose content is an alignment. whether the file. bam it compressed? if

snp database

updated 11.0 years ago • hudarembang

all the reads other than properly paired? 1. My post processing steps are as follows: Sam to Bam conversion and take only properly paired reads Bam Validation Sorting of bam file with sorting order "queryname" (because...Due to this later stages of my pipeline are affected. Surprisingly GATK is working with truncated bam file with some error at the last line. So what I am missing, I do…

R next-gen sequencing software error

updated 7.0 years ago • vivekruhela

Sorry friends, I have a sorted bam file, I entered ``` [izadi@lbox161 izadi]$ $BED/bamToBed -i eg1_highquality.sorted > eg1_highquality.bed Failed to open BAM

bed bowtie bam

updated 3.1 years ago • Angel

Hi, when use diffbind to check ChIP-seq data we need bam file. Do I need to use the bam file which already removed unmapped reads /duplicates/blacklist? And what will be the right

ChIP-Seq R sequencing

updated 6.8 years ago • mikysyc2016

about this, but I didn't get my answer complete. https://www.biostars.org/p/399693/ I have 6 bam file that one of them is just 2 Mb and one is 2 Gb. I think the comparison between VCF file of these bam files is not fair, because...they don't have equal read. so I want to merge all the reads ( probably bam files) to a single file and then get the VCF file output of this. I want to do following c…

SNP samtools bam vcf

updated 5.5 years ago • khatami.mahshid

Hello, I need to add CB tags to my bam files. Below is what I'm doing. I see the tags when I pipe to stdout but the tag is not written to the new bam. What is it that I'm missing...Thanks! ``` # $LINE is the path to the original input bam, there is one bam for each $cell samtools view -h -b -o ${cell}.bam ${LINE} | sed -e "/^@/! s/$/ CB:Z:${cell}/" # or samtools view -h -b ${LINE} | sed -e "…

samtools bam

updated 11 months ago • Maria

Hi, I had ChIP seq data that I aligned using STAR and got the bam files for and ran peak calling using macs2. I see a list of regions that are enriched, however, when I use the bam file for my...Hi, I had ChIP seq data that I aligned using STAR and got the bam files for and ran peak calling using macs2. I see a list of regions that are enriched, however, when I use the bam file for my IP an…

ChIP-Seq

updated 3.5 years ago • aropri

Is the following the correct process? I do not believe I can "convert" .bam to .bed directly. I am converting .bam to vcf using bcftools, and then using plink to prepare .bed and .fam files. bed to vcf using

bed bam vcf

updated 6.7 years ago • genomics Newbie

Hello, I have a lof of bam files (nearly 500) each 10GB. In total my data occupies 7T. I know bam files are already compressed. Does it make sense to compress

bam

updated 5.1 years ago • User000

barcoding. Is there a way to call variation on this mixed sample file? I already did a simple bam-readcount and it gives too many possible variants at each site. I figured I need a true variant caller to distinguish true

pacbio long reads SNP

updated 6.4 years ago • nchuang

if the deletion is located at position 2, samtools gives me that is at position 1). I've tryied bam-readcount to do the same task and it calls INDEL at the right position (after check it with IGV). What I've tryied so far is: - Using

samtools mpileup variant calling count nuceotides

updated 5.7 years ago • vit.filippo

Hi, I have 100's of BAM files in a directory. Is there a way with which we can convert all the BAM files in a directory into sam files. I know that we...can use samtools view -h <path .bam=""> > <path .sam=""> to convert individual files. Thanks </path></path

bam samtools sequencing

updated 2.1 years ago • venks

Hello everyone, I here use BioStars to ask a question. I would like to extract the data from Bam files and already succeeded in retrieving the data from small Bam file (<1Gb). But I couldn't extract the nucleotide data...from relatively large Bam files (about 10Gb or more). My question is what is the reason for this. The problem of PC spec?? I used Ubuntu installed to windows...10. I co…

software error bam sam

updated 5.3 years ago • cdc421

Hello, I have aligned around 3 varieties against 5 different reference genomes. Now I have several BAM files. What I want to do next is to see if there are different SNPs in different varieties and references (in the same region...Hello, I have aligned around 3 varieties against 5 different reference genomes. Now I have several BAM files. What I want to do next is to see if there are different …

RNA-Seq bam

updated 5.3 years ago • User000

Hello, I have selected for certain chromosomes from my bam file. Now, I would like to change the header as I want to do the SNP calling, which means I want the header to only contain the...Hello, I have selected for certain chromosomes from my bam file. Now, I would like to change the header as I want to do the SNP calling, which means I want the header to only contain the chromosomes that I ha…

bam

updated 10.2 years ago • hpapoli

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