Questions tagged [sam]
Use this tag for questions specifically related to the text SAM format. For general questions about the SAM/BAM formats use the tag BAM.
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Convert 10X VDJ .bam file to .fastq
I asked a similar question in the past regarding the conversion of scRNASeq .bam files to .fastq's, please refer to this link here: BAM to gene expression matrix (UMI counts per gene per cell),10X
I ...
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How can I convert all the bam files in a directory into fastq files using samtools bam2fq?
This question was also asked on Biostars
I want to find variants in the exome data. How can I convert all the bam files in a directory into fastq files using samtools bam2fq?
I couldn't find simple ...
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How to subset BAM file based on read length range (120-180) bp?
Hi I'm wondering how I can subset a BAM file based on read length. Precisely I want just read lengths of 120 to 180 bp reads in the new BAM file.
I'm trying several way, but none of them giving the ...
- 309
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Problem while mapping reads to mtDNA (SortSam)
I am trying to map MiSeq reads to a reference genome and extract mutations using MToolBox, which implements gsnap, GATK, Picard, and other tools. When running the tool with example data, there were no ...
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Pysam - fetch reads within region
I'm using pysam (and also samtools) to find all reads in BAM files that are within a specific region py_bamfile.fetch('4',42266768,42268410) and the following read ...
- 53
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Discrepancy in Read Counts Between FastQ and BAM Files in Adapter-Trimmed Pipeline
In a FastQ to BAM pipeline where only adapter trimming is performed, I've noticed a potential discrepancy in read counts between the initial FastQ files and their resulting BAM file. Specifically, I'm ...
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Generate simulated bam for certain snps
I want to benchmark my DNA sequencing pipeline. In order to do that I want some gold-standard files in every step(.vcf,.bam,.fastq). I want to generate/simulate a bam file of reads for a given set of ...
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low mapping percentage in bwa mem
After aligning paired-end reads to a reference genome, I am getting low percentage:
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- 103
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obtaining a fragment data file bed from bam
Im trying to follow this pipeline https://github.com/epifluidlab/cragr on cfDNA WGS. I have bam files from paired end reads aligned with bwa mem.
The workflow requires bgzipped and indexed fragment ...
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How to reduce BAM
Consider a sorted, indexed, only mapped reads containing BAM file.
Is there a way to get a sub BAM based on read line numbers?
This can be done iteratively using a counter but its too slow. Is there a ...
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STACKS ref_map.pl no BAM records
I have 133 aligned and sorted BAM files that I am trying to run through the ref_map.pl script from the STACKS pipeline. My script looks as follows:
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Check mutation of a gene
Hi all, I am checking if a gene which around 50k base pairs has mutation. So is that a variant from A to G? Would you please tell me how to do so? Thank you so much!
The reference sequence from GRCh38,...
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Gviz Coverage Plots
This question has also been asked on Biostars
I have two bam files from single-cell RNA sequencing mapped to the reference genome using CellRanger, I can view them in IGV and I have a particular ...
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Off-target % for whole-exome sequencing panel
My samples have been sequenced with the Twist Exome 2.0 sequencing panel, and I want to assess how efficient the sequencing has been. By efficient, I mean examining metrics such as the uniformity (...
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