Biostar

9,196 results • Page 11 of 184

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 3.6 years ago • optimistsso4co3

Dear all, this may be simple for others, not for me... Is there any way to filter out reads from a bam file based on a gff3 file information? My purpose is to get out the microRNA info from bams to run analysis without this 'contaminating

bam gff3 filter RNA-seq

updated 8.2 years ago • sgmiriuka

I have some bam files of RNAseq data, and I want to calculate the FPKM values of each gene. However, I couldn't know how the bam files are generated

RNA-Seq software error

updated 9.9 years ago • EileenXu

I would like to view a SRR038263.sra BAM file in samtools and do alignment to reference genome. How could I view the SRR038263.sra in samtools? I have already install...and make samtools at same directory where I have SRR038263.sra BAM file. I would be glad for your kindness and support. Regards, Rocky

samtools alignment

updated 13.8 years ago • Rocky

to find tools like Bedtools, Samtools, etc that calculate the coverage and depth statistics for a BAM file. But I am looking for a tool that will plot them for my BAM file. I tried a tool called BAMStats (http://bamstats.sourceforge.net...This tool did not work on my BAM file - it errored out saying "too many reference files". My BAM file is from viral samples so there are many reference genomes

bam coverage depth next-gen-sequencing

updated 2.4 years ago • kay

However, I also needed the genomebam files which where given to me later. I noticed that for the bam files the kallisto command was run differently. The first files were run without `-b` but when the bam files were generated...they were run with `-b 100`. Would the bootstrap option change anything on the BAM files? I just want to visualize them on IGV to check if my knock out has worked. I am not…

RNAseq kallisto BAM

updated 2.5 years ago • bioinfo

ChIP-Seq data and am interested in doing quantile normalization. I created bedgraph files from my bam files using bamCoverage with a window size of 50 bp so that I get the number of reads for every 50 bp of genome. However I noticed...that every bam file has a different number of lines (even after I split up the intervals that bamCoverage automatically merged) so I cannot...with a bed file I cre…

ChIP-Seq normalization bam

updated 3.1 years ago • ej

DNA Methylation files here https://portal.gdc.cancer.gov/legacy-archive/search/f. But they only have BAM files here. I need fastq files for these BAM files. I have contacted GDC and they said they only have BAMs available. Since...fastqs in bisulfite context are aligned with Bisulfite-aware aligner, I don't think converting BAM to fastq is straightforward. I tried using samtools bam2fq function a…

Methylation Bisulfite-Seq TCGA BAM

updated 6.8 years ago • divyswar01

file (remapped) and find the depth of coverage for that bam file (`samtools depth -r chrM remapped.bam`) . This requires the bam file to be sorted, which is why I include that at the bottom...THE ERROR: (occurs when I call samtools depth on the sorted remapped bam) ``` [bam_pileup_core] the input is not sorted (reads out of order) [bam_plp_destroy] memory leak: 1. Continue anyway. ``` THE FUNCT…

sort bam samtools

updated 2.5 years ago • quachtina96

Hi, I'm trying to run a package called ATACseqQC, which already has an example bamfile within the package. However I'm wanting to run the package with my own BAM files. I'm new to using R, so I've probably done this completely wrong... I first loaded the Rsamtools library, and then tried to...has an example bamfile within the package. However I'm wanting to run the package with my own BAM files.…

R BAM input ATACseqQC

updated 7.3 years ago • siangoldie

I have bam files that I have split into unmapped, uniquely mapped and multimapped bam files from HISAT2 alignment. I am trying to merge...the sorted unmapped and uniquely mapped bam files with the command samtools merge A1_merged.bam -b A1_unmapped.bam A1_unique.bam and am getting an error [E::hts_open_format...Failed to open file BAM?T samtools merge: fail to open "BAM?T": No such…

RNA-Seq samtools merge

updated 5.0 years ago • mar77

Hello. I have a question about Bam files. How can I extract the alignment of a specific named read from a Bam file? I did a search for Biostar and and found the...answer Question: (Closed) Efficiently Extracting Reads With Specific Names ('Queryname') From .Bam File https://www.biostars.org/p/68977/ ``` samtools view file.bam | grep queryname - > subset.sam ``` Yes. This is a simple an…

alignment

updated 4.7 years ago • 2xijok

I have some bam files and would like to use them for further analysis. but I want to do more analysis only on some of the genes not everything...in the bam file. I have a list of genes that I want to use for the next step. also in my list I have both gene symbol and gene ids like: AAAS...ENSG00000094914 ACO2 ENSG00000100412 I thought samtools can help to get such a bam file (like the fo…

alignment

updated 8.5 years ago • Sara

Any suggestions on good programs or scripts to convert a BAM file back to a fastq? I have found some scripts but wanted to ask for advice before I go too far down the wrong path

next-gen-sequencing fastq

updated 24 months ago • Zach Stednick

Hi! I would like to convert fastq file to bam i in oneliner: I have tried: bowtie2 -x {input.index}/hg19.zip -U {input.fastq} | samtools view -b -o {output} but it does not work. Anyone

fastq bam

updated 3.1 years ago • ja4123

Dear all, I have one problem, I would like to count the content of GC nucleotids from bam file for each read. I think I have to count it from $10, but I do not know how? Could you help me please? Thank you

gc bam awk perl

updated 11.4 years ago • filipzembol

Hello, I am mapping RNA seq data using STAR and wanted to extract the unmapped reads to map against something else later in the pipeline. I used the following to create the genome to map to: STAR --runThreadN 20 --runMode genomeGenerate --genomeDir /media/genome/ --genomeFastaFiles /media/genomic.fna --sjdbGTFfile /media/genomic.gff --sjdbGTFtagExonParentTranscript Parent --sjdbGTFfeat…

RNA-seq STAR

updated 2.6 years ago • erik.burchard

a poolseq Fastq file and performing alignments using bwa aln, I tested a couple of the split bam files using Picard's ValidateSamFile tool and found the following errors: Error Type Count ERROR: INVALID_MAPPING_QUALITY...1 ERROR: MISMATCH_FLAG_MAT_NEG_STRAND 4419 ERROR: MISSING_READ_GROUP 1 When the split bam files are concatenated into a single bam file, the errors t…

picard GATK bwa

updated 3.9 years ago • shpak.max

Hi there! I am trying to convert my SAM file (7.5G) to BAM format using this line of code: samtools view --threads 4 -buS ${sample}.sam -o ${sample}.bam My first issue is the memory requirement

samtools

updated 2.0 years ago • kb_93

In order to use genomic data in IGV I converted SAM files to BAM and them executed the index via samtools. I observed that when generating the index from the same BAM file the output could

genome assembly next-gen

updated 5.2 years ago • carolina.santiago.t

Hello! I'm working with a .bam file and I want extract line by line. I'm trying to use the following bash command: ``` for line in `samtools view filename.bam...do something done ``` but it doesn't works because the variable line will be a single field of .bam file. How can I assign at variable the entire line? Thanks

bam samtools

updated 2.2 years ago • User 4133

Can anyone help me reading the reads values from a BAM file? I need to analyse a bam file with java and PICARD, retrieving this information,but unfortunately I have no idea how

bam java

updated 2.5 years ago • Jesse

we would like to translate the genomic sequences in a bam file to its protein sequence (all six frames). We would like to do it while keeping the structure of the bam file ( or at least

bam protein translate samtools

updated 5.1 years ago • Assa Yeroslaviz

with Maxbin2. On the annotated genes, I then used BWA together with the raw FASTQ files, to obtain a BAM file. Now, how do I interpret the bam file? The main goal is to find the depth for each of the genes that were annotated with Prokka

bam samtools prokka bwa

updated 5.7 years ago • Hansen_869

It is easy to get allele frequency for a site (mutation/snp etc.) from a bam file. How do we get the allele frequency of a gene (in some metric) from a .bam file, like dominant allele frequency of a gene, for

allele frequency

updated 7.4 years ago • Kasthuri

Hi, I got an indexed and sorted bam file from a colleague, and I also have the reference genome. My question is: how can I get a full sequence (eg. fasta file) from...the bam file? I googled some tools, but most of them are used to convert bam file into fasta, and the fasta file still contains segments

Assembly alignment sequencing

updated 7.1 years ago • wang.yiguan

Hello all, I want to sort my bam by queryname so i used the command: Samtools sort -n -m 1 -@ 10 -o /Path/ouput.bam /path/input.bam It's work fine but at the end the...Hello all, I want to sort my bam by queryname so i used the command: Samtools sort -n -m 1 -@ 10 -o /Path/ouput.bam /path/input.bam It's work fine but at the end the ouput.bam...is really bigger thant input.bam (7…

alignment genome samtools

updated 4.3 years ago • quentin54520

gt; > scaffold1 > > scaffold2 > > scaffold3 And an another file which is a bam file. Is there a tool that extract reads (or filter) that have mapped only on my target ? ( I have one bam with paired reads and one...bam with single reads

bam filter

updated 7.8 years ago • Picasa

I want to reduce my bam file, obtaining a new bam file that contain only loci in the bed file in input like chr1 30498890 34983248 chr2 30398890...test.bam | awk '$2 != 4 {print}' and intersectBed -abam file.bam -b test.bed but the source bam file isn't reduce dimension. How can I do

bam

updated 8.7 years ago • marcodpc

Hi all, I want to find HLA consensus sequence from bam file. Can I use bwa.kit to treat the bam file directly? Thanks and best regards, Michael

next-gen

updated 2.9 years ago • zengxi.hada

Hi, I want to ask how to convert the transcriptomic coordinate bam file to genomic coordinate bam. I mapped the reads to the transcriptome with bowtie2. One possible solution I found is that

bam genomics

updated 23 months ago • Ge

Hi, I'm doing a bedtools intersection between a BAM and BED file and am getting a few columns of output that I don't know how to interpret. Running `bedtools intersect -a <bam> -b <bed...what the other numbers are meant to signify. This particular output appears contingent on passing a BAM, as converting the BAM to BED and then running `bedtools intersect -a <bam bed="" converted…

bedtools

updated 3.9 years ago • Steven Mick

I have merged two different bam files with same @RG ids (with picard) When I looked into the bam file however, ![enter image description here][1] I found that the...name "test" has changed. I have matched the IDs for variant calling for one merged bam file. When I tried merging different bam files and did normal variant calling, the output vcf file had more than one sample...enter image des…

bam WGS variant calling

updated 3.0 years ago • askif4

packages/release/bioc/vignettes/ATACseqQC/inst/doc/ATACseqQC.html) on my own files; I generated BAM files from fast.qc files in linux. I have the lines of code in R (following what the author did): library(BSgenome.Hsapiens.NCBI.GRCh38...gal, outbam = shiftedBam_SS123) When I do so, I am getting the error that "seq levels(param) not in BAM header". I checked the header of my BAM file, and …

R ATAC-seq BAM

updated 5.0 years ago • sophia.dingg

How to get reference and alternate allele count from BAM file at a given chromosomal position

next-gen sequencing SNP

updated 5.8 years ago • mona11224

Can I merge two bams from different samples (biological replicates) using simply cat command

alignment

updated 4.7 years ago • kanwarjag

Are there any command line tools that specialize in predicting splice site variants from bams

splicesite wes

updated 8.5 years ago • vigprasud

sample using short read sequencing. The reads have been mapped to GRCh37 and I have created a BAM file suing GATK best practise workflow. I would like to do some benchmarking of Structural Variants > 20bp. I downloaded...giab/data/AshkenazimTrio/analysis/NIST_UnionSVs_12122017/ I would like to compare my bam file along with this VCF. However i see that the variant calls do not align co…

vcf bam

updated 2.5 years ago • anuradharavi10

Hi, I want to read in a BAM-file into R using the readAligned function from the ShortRead-package. However, I am just interested in the junction reads...reads.. I would need a filter for reading in junction reads without indels readAligned(".", pattern=.bam,type="BAM",param=param) Thanks for helping me out

r bam cigar

updated 12.8 years ago • lydia.herzel

I have scRNA seq data for three time points. I ran cell ranger pipeline that gives me one bam file I want to convert this bam to one bam per sample/cell. Is there a package or toll that can help to achieve this

RNA-Seq

updated 7.6 years ago • rob.costa1234

I am writing a Bash script that has the following aims: - Compare multiple BAM files (over 100) using samtools to obtain the number of mapped reads - Find the BAM file with the smallest number of reads - Based...on this smallest number, use seqtk to scale all other BAM files My problem is to do with how to parse through all BAM files. I am very new to using getopts and I can't get it to do w…

bam samtools seqtl getopts

updated 6.8 years ago • m98

After merging 6 bam files (samtools merge) I attempted to look at the read depth within a specific set of intervals and got the following error...not sure exactly why expect maybe the merge tool takes a sam and not a bam file? samtools depth -b --bed /sonas-hs/tollkuhn/hpc_norepl/home/rbronste/refGene/promoter_example.bed /sonas-hs/hpc_norepl...EOF marker is absent. The input is probab…

bam samtools sam

updated 6.6 years ago • rbronste

Hey guys, I was using qualimap to estimate the features of a .bam file. I input the .bam file and it reported like this: Failed to run bamqc java.lang.RuntimeException: The alignment file...Hey guys, I was using qualimap to estimate the features of a .bam file. I input the .bam file and it reported like this: Failed to run bamqc java.lang.RuntimeException: The alignment file is unsorted. Please…

alignment

updated 7.0 years ago • Yingzi Zhang

Is there a way to get freebayes to output the BAM file adjusted after haplotype assembly? Also, is there a way we can run it just to get the haplotypes and the changed BAM

freebayes

updated 7.9 years ago • cvniru

Dear Biostars, I have 45 directories, each containing 2500 bam and 2500 bam.bai files. Each bam file represents alignment results from aligning (shotgun metagenomic) sequences to a...reference fasta file. Many of the bam files are empty and only contain the header and no matching/aligned reads. Is there a way to remove these bam files that don

bowtie2 samtools BAM

updated 6.3 years ago • samlambrechts299

Hi everyone, I am currently trying to run the command in DANPOS3 - which is a software to analyse nucleosome positions and call peaks. This is the command $python3 danpos.py dpos [optional parameters] The bam file I am using was created using Galaxy. So the reads were aligned using Bowtie2 and then using "samtools view" I obtained only chromosome 5 reads. I validated this file for any erro…

sequence nucleosome danpos galaxy

updated 4.8 years ago • sshibin

Hi everyone, is it possible to convert between sam and bam file inside C++ code. I knowhtslib library offers implementation of file formats including sam and bam. However, I could not

bam htslib sam

updated 8 months ago • Uveyik

Is it better to use a fastq file or a TMAP aligned and unaligned bam and convert those to 2 fastq and combine them? The problem is a fastq is not created by default, but I want to make sure that...by converting the aligned then unaligned bam to 2 fastq files then combing them, that will be ok for bowtie2 or bwa-mem or gatk. Thank you

ngs alignment

updated 2.2 years ago • bioguy24

sequences I want to align against genomes in IGV. The preferred format for alignment is said to be BAM. Unfortunately I haven't found a straightforward way of creating BAMs straight from coordinates. I assume I'll need the

R genome alignment

updated 2.9 years ago • ad

Hi All, I have some PacBio data in bam format obtained from the Sequel platform. I know that the PacBio sequencing is able to captures the methylation information...but I don't know how to "obtain" these information. Is there a way to know which bases in the bam files are methylated using samtools? Or is there a compleatly different way? Thank You

PacBio methylation bam samtools

updated 7.1 years ago • gabri

9,196 results • Page 11 of 184

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