Biostar

9,144 results • Page 3 of 183

Hi, I have mapped reads against a reference with bwa and got a big bam file now. I would like to retrieve a separate bam file for every contig. I do not mean "I want 1 bam for every chromosome". A chromosome...I would like to get 2 bam files. How do I do that

sam contig

updated 2.3 years ago • Marvin

I have bam file that I must convert to bed file to filter specific reads. Now I need to convert output bed to bam file. I am using bedToBam...As an output I have bam file but when I visualize it I see that sequences are in headers. ![enter image description here][1] [1]: /media/images/7a7f3ae1...gt; ???????????????????????????????????????????? Is there any way to make this bed to bam …

bam bed

updated 3.7 years ago • kperlejewski

I am trying to create a BAM file merging two different BAM files simulating at different level of contamination. Suppose I have two bam files for...SampleA and SampleB. I want to generate 5 different BAM files at contamination level of 10%, 20%, 30%,40% and 50%. I understand that I should extract reads from one of the two bam files at...the given dilution percentage and reassign to the other bam …

NGS BAM

updated 8.6 years ago • MAPK

How can I separate a bam file into multiple bam files such that each bam file contains information for one cell using UMI-tools

bam scrna-seq umi-tools

updated 21 months ago • Researcher

I had 3 replicated bam files, and I merged them. I wanted to see if there is a way to reverse this (going from the merged to original bam files

samtools bam merge

updated 5.4 years ago • rsafavi

Hello, I am trying to create a smaller BAM file from the original BAM file. The smaller BAM file should have info on only about 10 loci. Can I not just append the `mpileup...output of the region of interest to the header (`samtools view -H <bam>`)? Any pointers on how I can accomplish this would be appreciated! Thanks</bam

bam sam RNA-Seq samtools pysam

updated 2.6 years ago • JameB11

Hello, So I've used salmon to extract readcount and use tximport to be used in DESeq2. After I perform DE analysis, there are some genes that has NA result. I suspects...Hello, So I've used salmon to extract readcount and use tximport to be used in DESeq2. After I perform DE analysis, there are some genes that has NA result. I suspects that this is caused by low count or maybe even 0 readcount …

deseq2 RNA-Seq

updated 6.3 years ago • bharata1803

This might be a very basic R question.. [QDNAseq][1] creates 'readCounts' R object which holds all of the samples, yet I wish to create a chart for each sample at a time e.g. isobarPlot(readCounts

updated 6.7 years ago • roy.granit

dream3-settings 1 > myvar.fpfilt.vcf And I got the following output: Loading readcounts from mybam.readcount... Parsing variants from myvar.snp... 672 variants in input file 672 had a bam-readcount result...663 had reads1>=2 0 passed filters 672 failed filters 0 failed because no readcounts were returned 0 failed minimim variant count < 3 …

fpfilter varscan2

updated 5.8 years ago • ar.satkhol18

Recently some of our BAMs have come through with duplicate SQ tags in the headers. This caused some of the downstream tools to fail. We now want a...Recently some of our BAMs have come through with duplicate SQ tags in the headers. This caused some of the downstream tools to fail. We now want a tool...to check that the BAMs' headers conform to SAM/BAM Format specs. The Picard/GATK ValidateSamFi…

headers BAM

updated 2.8 years ago • sbilobram

I have a genome assembly in fasta format and the mapped reads in bam format. I want to use amosvalidate to assess the assembly, and as a result I want to create the afg file. Is there any tool that...I can use in order to create afg from bam file

bam genome assembly

updated 11.4 years ago • bioLife

Is there anything software which can convert two SE alignment bam files to one PE bam file? My SE bam files are from BWA mem

alignment bam bwa

updated 6.0 years ago • mynameliuxiang

I am trying to convert some SRA files to BAM format but I have a problem. How do I convert a FASTQ file to BAM file? I've been trying for some time and I wrote the following...sra` samtools sort $1.bam ${DIR}/foo samtools index ${DIR}/foo.bam rm $1.fastq $1.bam ``` I get a BAM file but it has no header: ``` samtools view -H foo.bam @HD VN:1.4 SO:coordinate @RG ID:A SM:sampleName `…

bam fastq sra

updated 2.5 years ago • kumbarov

Hello. I have numerous bam files which I need to merge into a single bam file. How do I know whether I need to first index and sort the bam files

bam merge

updated 6.7 years ago • genomics Newbie

I am getting an error message with regards to a corrupt bam: ``` Error: BAM file is corrupt. Samtools cannot parse header ``` Does anyone know if there is a fix? Or do I have to realign the bam file

samtools

updated 5.2 years ago • vctrm67

Hello! I am trying to calculate some probabilities via python and for that, I need a bam file in it. I'd like to know what is the best way of uploading bam into jupyter notebook, so I can see how reads are laying against

python bam

updated 3.1 years ago • Anst

Hello everyone, I would like to ask a question. I have BAM files for each hg19 chromosome, but I need to create a fastq.gz file, so I can realign the reads to hg38 again. The SRA for the...ask if anyone has done it before and how to create one pair of paired-end fastq.gz files out of 23 BAM files. Do I need to convert first to Fastq eahc BAM file separately and then combine corresponding fast…

fastq bam

updated 3.2 years ago • Qboy

Hi everyone i want to detect CNV from BAM file. My question is: in what level i can use BAM file to CNV detection. I mean, unsorted BAM or Sorted BAM or deduplicated BAM...Using Picard) or realigned BAM (using GATK) is better to CNV calling

CNV BAM

updated 7.0 years ago • reza

Hi all, I am trying to take a bam file, convert it to cram, and then back again to bam and have the bam before and after conversion to be identical. Using samtools...seqs.bam > seqs.cram samtools view -b -T ref.fa seqs.cram > seqs.bam When analysing the bam before and after, there are differences. The headers differ (md5 etc), which are of no concern to me, but the records act…

samtools cram

updated 7.9 years ago • bjarki.sigurjons

Hi everyone, I have some BAM files but not the original FASTQs. Normally, I use fastp to trim FASTQs, but it does not accept BAM files. I was wondering if...there is a way that can trim BAM files directly? Thank you

FASTQ BAM quality trimming control

updated 2.5 years ago • Kyle

Hi all, I constructed the variant calling pipeline for BAM file. However, when it was applied to positive samples, I did not find any well-known variants in the VCF file. What I am considering...is that there might be less-sensitive method in my pipeline. So I want to create a simulated BAM file based on the existed bam, just change the reads in the bam to create a variant, etc., rs6071. Is th…

simulated variant bam

updated 2.5 years ago • J.F.Jiang

Hello all. I am new to bioinformatics and needing some help. I have a Bam file generated from fastq, In the command I used, a sorted bam file is supposed to be created but I keep getting errors. I am...trying to split the BAM file (about 50GB) into several Bam files so I can sort it separately. But I don't know how to go about this. (I am a beginner ). Any help

next-gen alignment

updated 7.3 years ago • jaqx008

I have to open a fasta file and match it with a bam file in c++. Unfortunately i open the bam file correctly, but i have no idea how to open the fasta file and match it with the bam...Before beginning the matching, i havo to take care of some informations of the bam file: the quality of the bases, the read quality, the orientation of the read, the initial and final position of the read and...of t…

c fasta bam

updated 12.8 years ago • Pellix

mapping_pipeline/blob/master/Arima_Mapping_UserGuide.pdf][1]), I combined them to give a merged bam file (it also does other things like filtering for mapping quality, adding read groups and remove PCR duplicates). Now, the...from a HiC experiment, and I want to analyze them using HicPro, but HicPro cannot work with merged bam files, it needs separate bam files for R1 and R2. So, I wanted to kn…

RNA-Seq samtools

updated 6.7 years ago • c_u

When use DiffBind to compare ATAC-seq data we need bam file for sample sheet. What kind of bam file do we need? Can I use the bam file which already removed duplicates? OR just primary

DiffBind ATAC-seq

updated 20 months ago • Miao Zhang

I have two BAM files that have a different sample in read group (@RG) section. I would like the sample to be the same. How can I quickly modify...the sample of the read group in a BAM file, so the merge BAM file has a single sample

bam

updated 9.9 years ago • rickyflintoff

Hi, I have around 20 BAM files and each of them have proper bam header including RG ID, Sample, Library, Platform unit, Description and Platform. I...Illumina, Solid, ABI_Solid, and CG. But I wanted to be quiet specific when I was converting SAM to BAM and used "Solid5500XL" as the platform name. I know there are AddorReplaceReadgroups and ReplaceSamHeader coomand in...Picard which I can use t…

bam

updated 2.6 years ago • Ashutosh Pandey

Dear All, I am trying to use the bam-window for the first time to prepare the input files for the copyCat package for CNV calling. I do not see much of a documentation...resource for running the bam-window. I tried to run on my tumor bam file and was thrown with an error. I would like to know if anyone has information for a...if anyone is willing to answer here I would just put the command and t…

bam-window bam exome CNV

updated 4.0 years ago • ivivek_ngs

How do I know if my .bam file is sorted? If it is not, how to sort bam? Thanks

sequence

updated 8.1 years ago • valopes

I am using `bcftools` to make `vcf` from `sorted bam` using: bcftools mpileup -Ov -f ref.fa sorted.bam | bcftools call -mv -o sample.vcf But I want to make a single `vcf` from multiple...sorted bam` files using `bcftools` with SNPs from each `sorted bam`. Thanks

snp

updated 5.6 years ago • evelyn

Is it possible to merge a Solid F3 and F5 bam into a paired end bam??? The paired end reads have been mapped seperated by bwa 0.5.9 and for a downstream analysis I need a...bam that contains the paired reads. Or redoing the mapping the only option

bam solid

updated 12.6 years ago • William

offer the best performance for converting to and from CRAMs? * Do people have to re-index their BAM after converting from CRAM? ``` # 1) Convert BAM to CRAM samtools view -T ${FA_REF} -C -o ${cram} ${bam} # 2) Store CRAM & discard *.bam/*.bai # 3) Retrieve...CRAM from storage and convert to BAM samtools view -T ${FA_REF} -b -o ${bam} ${cram} # 4) Re-index BAM to include CRAM-added h…

sambamba bam cram samtools

updated 23 months ago • DavidStreid

Hi there, Just wondering, is there somebody can explain how the BAM Index made? I tried to read the samtools code so I can understand how samtools create the index for the BAM file but still...don't understand. How actually the creation process of the *.bai file from BAM file? Cheers

BAM Index samtools

updated 7.0 years ago • t.marvin.christian

Hello, I have question during analyzing eCLIP-seq data. Someone converted BED file to BAM file during analyzing. Can I try analyzing this BAM files? I concerned that BED are about 3GB, but BAM are just 80MB. I've known...that there are many information in BAM file, and I've heard that it's not good for converting BED to BAM file. Is it okay using this BAM files

rna-seq eCLIP CLIP

updated 4.8 years ago • dahun73

Dear all, I have one bam file produced from single end RNAseq reads using Gsnap. I want to extract the separated bam files for sense and antisense...reads only. I know that the samtools could use to extract them by flag for pair ens read bam file. But what's the flag number for single end reads bam file? what's the commands for single end bam file? Or what other tools...could be used to extrac…

RNA-Seq

updated 2.8 years ago • wu.zhiqiang.1020

Hello everyone, I have 50 BAM files, some of them single-end and some of them paired-end. Well, I want to make a single bigwig file by combining reads from...all of these bam files. For this, I merged all bam files to a single giant bam file(700GB). However, I am getting out of memory issues while sorting...this giant bam file. 1. Is there any way I could sort this huge bam file? 2. Is it ok …

bam samtools bigwig

updated 2.1 years ago • Rajendra KC

Hi, I have an alignment file in bam format from STAR aligner. I want to study Differential expression gens from this bam file, I need all informations like...values ECT for plotting heat map and volcano. Is it possible to make these plots from alignment bam file

RNA-Seq deg gene R

updated 6.0 years ago • bioz

Hi All... I am trying to sort a .bam file created by STAR. I am trying to use samtools sort. I use the following command... $ samtools sort *.bam -o *sorted.bam I get a common...Hi All... I am trying to sort a .bam file created by STAR. I am trying to use samtools sort. I use the following command... $ samtools sort *.bam -o *sorted.bam I get a common error I have seen when you …

Samtools

updated 21 months ago • joseph.landry

Thanks all, the problem is solved. it appears that the warning message is not related to the bam header and the header is there already. Hi everyone, I hope you are all great, I'm trying to convert my sam files into bam using...however, I'm getting an error message with each command that requires the header to be in the bam file. (for example, running bedintersect: bedtools intersect -s…

samtools bam reheader sam

updated 21 months ago • S.O.T.AL-HASHIMI2

about before, but I plan on using `samtools reheader` to replace the chromosome notation in my bam file (from b37 to hg19). However, between b37 and hg19 headers the number of chromosome sequences is different and they are...in different orders. Can I: 1. Delete all the sequences in the b37 BAM file header 2. Add all the sequences from the hg19 BAM file into the edited b37 BAM file Will this w…

bam

updated 5.1 years ago • vctrm67

Hi, How to adjust BAM header after extracting only mapped reads from BAM files to have only the reference ids which are present inside the BAM

bam samtools

updated 5.1 years ago • Ric

Dear all, I have 100 .bam files and I would like to change all their header with a new header. The new header is the same for all files. The only one thing...different is in @RG: ID="bam file name" and SM="bam file name". How can I do this step instead of reheadering one by one? Thank you all for any help

bam header

updated 6.0 years ago • Huynh Nguyen

Hi, I am using bowtie + samtools pipeline to call snp. Split bam file and call snp by chromosome will save a lot of time. But the reference genome have many scaffold, split bam by chromosome...will produce a lot of scaffold_bam file. Now I want to split bam by scaffold, so the scaffold will split into one file. Is there any way to do that? I tried to use command: samtools view in.bam

snp genome

updated 2.6 years ago • l0o0

again with one more naive question. What according to you is the best way to normalize multiple BAM files to one another? My goal is to simply normalize a set of BAM files, then plot the avg read coverage. I've attached an example...of a read metagene plot showing the avg read coverage with BAM files that are **not** normalized to one another. To reiterate, my goal is to normalize these…

bam

updated 3.3 years ago • kstangline

So please, if you could answer me in the most simplest form I would trully appreciate it. I have two bam files (bam 1 and bam 2) that were generated when I aligned one fastq read file to two reference sequences (ref 1 ref2) fasta format...When I view my sorted bam file in IGV , I am unable to see how many reads were aligning to ref1 and ref2? I have a virtual ubuntu machine that I am using

alignment sequencing

updated 4.6 years ago • priscilladraj

Hi, I have set of sam files and I would like to convert them into bam files with the following script. But it didn't create bam files? What I have made wrong? ``` for file in `ls ~/wgs/sam`; do ~/bin/samtools...0.1.18/samtools view -bS ~/wgs/sam/$file \ > ~/wgs/bam/$FILE.bam; done ``` Thanks

bam sam

updated 2.2 years ago • Haluk

I have multiple bam files from cancer datasets and I want to check their quality. What I did was, I converted the bam to fastq using bedtools. I...got two fastq read files (paired end) per bam file. Now I checked the quality of the fastq files generated using fastqc tool. This is how I am trying the find a good dataset

sequence alignment

updated 7.1 years ago • banerjeeshayantan

Specifically, I notice something is wrong because the files have 0 memory in them when they go from bam to sortedbam. I have compared all the files during previous steps, bam, sam, and fastq. The ones which are stuck are of a comparable...SBATCH -o Report-%j.out cd $SLURM_SUBMIT_DIR ml picard/3.0.0 for i in $(ls *.bam | rev | cut -c 5- | rev | uniq); do java -jar /usr/local/…

bam dna

updated 15 months ago • mgranada3

I have been suggested to use the .phylip alignment file type. I currently have my data in .sam and .bam file types. I haven't been able to find any ways of converting .bam to .phylip (apart from a module called bioscripts.convert...analyses servers don't have this module). Are there any intermediary file types I have to convert .bam into first? Or are there ways to directly convert .bam file to…

bam phylip

updated 7.2 years ago • miles.thorburn

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

9,144 results • Page 3 of 183

Recent Votes

Answer: Reasoning - Why is it invalid to compare ratios of TPMs?

Snakemake version 8.27.1 on LSF cluster

Minimal Quality Control Thresholds in Shotgun or Amplicon Metagenomics for non assembly based analysis

Metagenomics/amplicon sequencing: Most publicly available data already host removed sequences or no?

Guided genome assembly

Answer: VCF filtering with Allele Balance (AB) using FilterVcf (Picard)

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