Biostar

9,146 results • Page 5 of 183

I'm starting to explore mapped sequence data formats. Specifically the possibility of replacing bam files with cram files, as bam and/or ubam files are generally quite heavy. Thus can affect transfer and computational times...have any experience with similar situations where the cram files will closely resemble the original bam/ubam files. In other words, can cram files be used as alternative to …

CRAM

updated 3.4 years ago • joe_genome

I have more than 50 bam files and wanted to extract the reads from a region from all those bam files and merge the outputs into a single bam. I'm using...view -b sample1.bam "Chr10:19000-46500" > sample1_intregion.bam I tried doing like below for all bam files: ``` #!/bin/bash for f in *.bam do samtools view -b $f "Chr10:19000-46500" > $f_intregion.bam done ``` it is not wor…

bam rna-seq

updated 16 months ago • Vasu

For prediction of lncRNA, I have 6 bam files from different group of the experiment. I need to do assembly using StringTie software. Should I merge file first...by one. And what is the advantages of merging them. I tried to merge them but it give me error that bam file does not have valid header

bam assembly lncRNA

updated 14 months ago • walaa.shalan

literate so this program has been difficult for me to get running. I am having issues with my bam-list file for the bmr calc-covg command in Genome MuSiC. From the description, it says that that this should be a tab delimited...file containing sample names and normal/tumor BAM locations [samplename normalbam tumor_bam] which (I think) I have created. My file has the format as follows: 850400…

genome music

updated 12.4 years ago • will.lockwood

Hi, I am trying to realign some of the bam files (paired end) using the following command. But I am getting error: [fread] Unexpected end of file ```r bam.files <- list.files...pattern = ".bam$", full.names=T) for( I in 1:length(bam.files)){ system(paste("bwa aln -t 22 ref.fa -b1 ", bam.files[i], ">", gsub(".bam", "_1.sai", bam.files[i]))) system...paste("bwa aln -t 22 ref.fa…

alignment sequencing R

updated 2.3 years ago • ifudontmind_plzz

Hello dears all, I have some BAM files from different samples which they have been mapped to the genome reference using bowtie2. Actually now I want to...merge these bam files so that the out put will be a single .bam file. I will be so grateful if you can help me in this purpose. Regards, Omid

SNP next-gen alignment BAM SAMtools

updated 5.4 years ago • jaafari.omid

Hi, I would like to randomly sample *with* replacement from bam files. One way to do that would be to convert the bam files to sam format and use python's np.random.choice. Is there a more...direct way to do this that doesn't require bam to sam conversion? Something like `samtools view -s` but with replacement? Thank you for your help

bam sample with replacement

updated 6.8 years ago • harleen.sn

Hello everyone, Can someone explain me how to use Hadoop BAM. I am new to this field. I would really appreciate the help

Hadoop bam hadoop genome

updated 5.3 years ago • shalini.ravishankar

100,000,000 reads, so when my first processing is done, I check if they are good to go. When the bam files are not over 100,000,000 reads, I sequence those libraries which are more needed. Here are the questions. 1. If I suppose...my library, sample, sequencing machine and everything is the exactly the same, are the bam file which is merged after mapping and pre-merge fastq file, then mapped bam…

sequencing bam merge

updated 7.0 years ago • woongjaej

Hi, I'm not able to sort the bam file correctly using samtools sort. My bam file size, increases after sorting ? Aligner - LAST Dataset- Human genome dataset...I generated a MAF file which I converted further in to sam ---> bam converted ---> sorted bam (problemetric) 1) Converting LAST output, MAF to sam ./maf-convert sam last-941/src/SRR2928269.test.maf...sort -@ 10 SRR29…

Assembly genome next-gen

updated 6.7 years ago • pinn

I have been given access to some bam files that have been compressed to the "ID.bam.spec" file format. I have not worked with this format before and cannot find...the necessary code to convert them from .spec to .bam A former colleague mentioned they used the spec-1.3.2 package to convert from .spec to .bam however, I am unable to find this

bam file-formatting spec

updated 4.5 years ago • gmora

To practice the command line skills, I want to test the EstimateLibraryComplexity after double the bam. I have one bam file (1.bam), copy paste it (name it 1copy.bam), then merge 1.bam and 1copy.bam by using picard-tools MergeSamFiles...I use samtools flagstat check all the numbers are doubled. The question is 1, why the merged bam size is not doubled? 1.bam is 79Mb, but merged bam is only 84M…

merge picard tools

updated 8.6 years ago • Joe

I would like to pass in bam files `pair_id.sorted.bam` and their corresponding index files `pair_id.sorted.bam.csi` into a nextflow workflow...I would like to pass in bam files `pair_id.sorted.bam` and their corresponding index files `pair_id.sorted.bam.csi` into a nextflow workflow. However...operator only for fastq file pairs? nextflow.config: input = "${directory}/*/*.sorted{.bam,…

nextflow bam

updated 20 months ago • Eliveri

my fastq files to hg19 using this command: bwa mem hg19.fa /DATA/myfile.fastq.gz then I made bam files from sam files using: samtools view -Sb myfile.sam > myfile.bam then I sorted the bam files using: samtools sort myfile.bam...myfile.sorted.bam and now I am trying to index the sorted bam files using: samtools index myfile.sorted.bam but I got this error: [ba…

genome alignment

updated 5.8 years ago • Sara

Hi I have merged bam file which has 24-101 bp reads. I would like to find the alternative splice events using MISO. I need to filter the reds in...Hi I have merged bam file which has 24-101 bp reads. I would like to find the alternative splice events using MISO. I need to filter the reds in my...merged bam file and keep only reads with 100 bp length. Is there any way to do that? Thanks in adva…

RNA-Seq

updated 2.7 years ago • hana

Hi all, I need to randomly pick up one read for each position in a file bam, do you know any way to do that? I saw there are different tools for setting a specific proportion of reads, but I need a new...bam file with only one random read for each position. Thanks for the suggestions

BAM Downsample filtering

updated 8.0 years ago • Simo

my trimmed RNASeq reads with human and mouse genome to get alignment file (accepted_hits.bam) in bam format using tophat. I provided htseq-count tool with two different bam files (sorted and unsorted). Case1: I used the accepted_hits.bam...directly as the input to the htseq-count and counted the reads for each gene. $ htseq-count -f bam -s yes -i gene_id accepted_hits.bam hg19_genes.gtf &am…

RNA-Seq htseq-count sequencing SNP

updated 2.7 years ago • nalandaatmi

Hello, on the TCGA website it says some BAM files may not have the unmapped reads available, how can I figure which BAM files may not have this? Also would I need to convert...BAM to FASTQ to access the unmapped reads? If I need to convert to FASTQ, isn't it better to use the FASTQ files available on the

unmapped BAM read TCGA

updated 3.8 years ago • Taktak31

and B runlevel data merged. Can anyone tell me the command/tool which i can use to merge flowcell A bam to flow cell B bam. My bams are indexed and sorted. Thanks

illumina hiseq bam merge

updated 13.8 years ago • Hmm

I have 30 + bam files and I have merged the data using samtools merge(adding RG tag using -rh option).I ran mpileup on each of the .bam files...in the merged case where n is the number of samples .However,I see my average coverage on the merged bam dropping to roughly half the value and some of the bases included in individual samples pileup are not included in the...merged bam pileup.I am not su…

samtools coverage bam

updated 9.1 years ago • Kssr

Hello, am trying to trim the reads aligned to the genome from my bam files of different sizes (50 and 80 nucleotides). Am doing this with bamUtil: ./bam trimBam subset.bam subset.80.bp.from.Right.fwd.80.bp.from.left.rwd.bam...R 80 ./bam trimBam subset.bam subset.80.bp.from.Right.fwd.80.bp.from.left.rwd.bam -R 50 the problem is that when i upload...in IGV the new bam file with the…

BAM bamUtil Trim

updated 8.0 years ago • fusion.slope

I'm using the gatk4 standard pipeline to create .bams from paired end fastqs using cutadapt and bwa 0.7.16 to hs37d5. The pipeline runs without errors and I get .bams of the expected...size. However, when I view them in igv hg19 they look like this, everywhere: ![Rainbow bam image 1][1] ![Rainbow bam image 2][2] [1]: /media/images/14e3a368-175f-451d-aab6-d77c4594 [2]: /media/images/ba2c…

alignment bwa gatk

updated 3.7 years ago • Siddharth

Bam file could have two different file extensions depending on the tools. Given bam file test.bam, - test.bam.bai secondaryFiles...bai] - test.bai secondaryFiles = [^.bai] For a flow to work with both kinds of bam inputs, how to set the secondaryFiles? Since secondaryFiles items must be present, it is not possible to set the secondaryFiles...to handle bam input from any bam index co…

cwl

updated 7.6 years ago • liuxf09

Hi Biostars, Does anyone know how to subsample read from a bam file? The below command gives the read number of this bam file. I want to get about 100,000,000 read out of 122,441,229 read. ![enter...provides similar function with fastq file like the command below. I was wondering if I can find a bam file version of seqtk. ./seqtk sample -s101 /data/long_read/lr_consoritum/pcb/ENCFF563QZR.f…

bam subseq

updated 24 months ago • Jjbox

Hi all, How do I check the coverage of bam files? These files are bam files derived from GTEx rna short reads. For fastq files, you can count the number of lines and divide...by 4 to get the reads wc -l / 4. Is there anyway to get read coverage from bam files similarly? ``` SRR1092349.bam SRR1366519.bam SRR1455653.bam SRR820448.bam

bam

updated 6 months ago • shinyjj

previously aligned using cellranger. Is there a way to use Monovar without splitting the cellranger BAM output file into BAMs for each individual cell, so instead just using the original BAM with the cell barcodes annotated

SNP single cell

updated 5.3 years ago • gnomee

like to make a bref file from a vcf file. And I have to phase the reference panel for that. Is a BAM file required for phasing by GATK? Is there a way to do phasing that doesn't require a BAM file? Thank you

imputation GATK phasing Beagle

updated 16 months ago • risah

Hi, Is there a tool to intersect multiple bam files to extract only the alignment that are find in all the bam files ? And maybe is it possible to specify a percentage of

bam alignment

updated 13.4 years ago • Nicolas Rosewick

bigwig files I have list coverage scores with 1bp span. These bigwig/bedGraphs were generated from BAM files that I don't have, but can I re-create those BAM files from BigWigs? Thanks

bigwig bam

updated 12.7 years ago • ashis.csedu

Hi, can someone explain to me about chunk in bam index file (*.bai) especially about the value from chunk-beg and chunk-end? What is that value? I still cannot figure it out about...I still don't get it about the value of the beginning/end chunk and how it relates to the bam file? Thanks

BAM

updated 7.6 years ago • t.marvin.christian

Hi, I have downloaded some specific regions from public database bam files. I would like to check if downloaded bam files are ok or truncated before transforming them to fastq files. I use samtools...to check the bam files. As I have several bam files, I would like to systematically check them and output the ones that are truncated... is there...any script for checking the bam files in a sys…

Exomeseq

updated 6.1 years ago • jonessara770

I need to revert a BAM file back to FastQ. Based on the GATK guide I need to shuffle first and then convert: http://www.broadinstitute.org/gatk...I need to revert a BAM file back to FastQ. Based on the GATK guide I need to shuffle first and then convert: http://www.broadinstitute.org/gatk/guide...article?id=2908 However, they don't mention anything about merged BAM files. How do you split a BAM…

fastQ bam

updated 3.4 years ago • crysis405

Suppose that we already have a set of SNPs called in a matched normal bam file, is there a way to extract the allelic depths in a tumour bam in the form of VCF without running variant calling in both...bams? I understand that this is probably not the best practice, but I think it could be useful in situations where the tumour

bam VCF

updated 3.2 years ago • mikothebichon

Hi, I have a problem with indexing the sorted BAM file in bwa alignment. I gave the command like this samtools index ~/Desktop/Ruelliasorted.sorted.BAM and says that EOF...marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). [bam_index_core] Invalid BAM header.[bam_index_build2] fail to index the BAM file. I …

bwa

updated 7.4 years ago • Gaurab2017

Hi, I have got a BAM file from PacBio data and would like to read some of the metadata of reads in R, e.g. ip, pw, rq. See here for pacbio BAM format: http...pacbiofileformats.readthedocs.io/en/3.0/BAM.html I have read the BAM into R with Rsamtools::scanBam('file.bam') and I have got a BAM file in R now but I don't know how to extract the ip, pw, rq info. I have...no problem extract sequencing…

bam pacbio rsamtools sam R

updated 7.8 years ago • cristian

muticov to find out Copy Number Variations among my samples, using the CANOES soft. I got many bam samples and canno't figure out how to "impute" a list of bams to bedtools multicov. Already tried the following `` find *.bam | xargs...bedtools multicov -bed probes.bed -q 20 > canoes.reads.txt An other way around: find *.bam > bam.list bedtools multicov -bams bam.li…

Bedtools

updated 8.0 years ago • benoit.tessoulin

Hi all, I downloaded the Denisova BAM file from [here][1]. Since this file is aligned to the 1000 genomes reference genome and I would like to align it to grch38 I...Hi all, I downloaded the Denisova BAM file from [here][1]. Since this file is aligned to the 1000 genomes reference genome and I would like to align it to grch38 I started the following utility for BAM to FASTQ conversion http://…

FASTQ BAM

updated 2.8 years ago • win

Hello, I am merging BAM files corresponding to several replicate experiments into one large BAM file. The resulting file is really large (400...quot; command, and at some point connection to the server broke, so it could be that the end of the BAM file is a bit damaged (e.g. not all parts of the individual BAM files which I was merging are included in the final BAM file...a small portion of read…

next-gen ChIP-Seq rna-seq

updated 9.1 years ago • biostart

Excuse me: I got bam file from targeted resequencing. So how do I know the start and end region from the bam file? Thanks for your help

sequence-alignment next-gen-sequencing

updated 2.6 years ago • 897598644

Is there a tool like bedtools shuffle which I can use to randomly shuffle a bam file? or will I have to convert my bam into a bed and then shuffle it? thanks

bam bedtools shuffle

updated 7.9 years ago • mparker2

Here is my attempt: def remove_too_long_reads(bam): for read in bam: if read.end - read.start < 60: yield read bam = BedTool(input.bam) bam = BedTool(remove_too_long_reads(bam...Here is my attempt: def remove_too_long_reads(bam): for read in bam: if read.end - read.start < 60: yield …

pybedtools

updated 8.8 years ago • endrebak

Is it possible to work on a part of a BAM file? Since these files are huge, I want to extract 1MB of the BAM file and convert it to SAM. My main intention is to extract...a meaningful part from the BAM file and then convert it to SAM instead of converting the whole BAM file to SAM. Thanks in advance for your answers

bam sam

updated 13.2 years ago • User 9906

I've got a few thousand small bam files produced against the exact same reference, and I want to merge them into one single big bam file. What is the best way...to do that? Should I do this iteratively or can I pass a long list of bam files to samtools/picard/etc in one go? Edited, since this is now partially solved. In my terminal, the methods below works...for up to 4092 files. More than that…

bam picard samtools merge

updated 3.7 years ago • 2184687-1231-83-

When I use samtools sort bam file, do i need to use samtool index the sorted bam file? what kind situation i need to use samtools index? Thanks

ChIP-Seq

updated 6.8 years ago • mikysyc2016

I have strand specific bam files of Riboseq data. I wish to convert it into bedgraph files - 1) Elongating coverage ; 2) Elongating A-sites. Can anyone help

Bedtools Bam

updated 2.1 years ago • prs

Hi, Can anyone please tell me how to turn bam gormat into WIG files? Also,WIG and wiggle- are they the same format? Thanks

bam

updated 8.5 years ago • blur

high PCR duplicates that I need to deduplicate with Picard MarkDuplicates. However, the outputted bam from Picard needs to be **un**sorted for the downstream program using the output of Picard. I tried running picard with ASSUME_SORT_ORDER...ASSUME_SORT_ORDER=unsorted and header sortorder=unsorted Either (1) is there a way to unsort a bam file from Picard? (2) is there a way to run Picard…

star picard

updated 2.9 years ago • wiscoyogi

Hi all, Im new to the ION Torrent technology and need your help to figure this out. The Ion GeneStudio™ S5 System generates **BAM** files as its primary output. when i need a particular **FASTQ** file, i can use the **FileExporter** plugin and get the relevant **FASTQ...Torrent technology and need your help to figure this out. The Ion GeneStudio™ S5 System generates **BAM** files as its primary …

NGS TorrentBaseCaller FASTQ BAM IonExporter

updated 3.6 years ago • Rajitha

I have a single bam file which was created by merging few other bam files. How can I get the names of bam files that were used during merging? Thanks

alignment sequence

updated 5.9 years ago • Rashedul Islam

How to convert bam to fasta? I have bam files and reference fasta. I want to get fasta sequence from bam file: ![see picture][1] Is there a software

bam fasta dna

updated 8.9 years ago • bbb

9,146 results • Page 5 of 183

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