Shulou(Shulou.com)06/01 Report--

This article is a detailed introduction to "how to convert fastq from bam files". The content is detailed, the steps are clear, and the details are properly handled. I hope this article "how to convert fastq from bam files" can help you solve your doubts. Let's go deeper and learn new knowledge together with the ideas of the small editor.

bedtools convert bam files to fastq files

bamToFastqTool: bedtools bamtofastq (aka bamToFastq)Version: v2.25.0Summary: Convert BAM alignments to FASTQ files.Usage: bamToFastq [OPTIONS] -i -fq Options: -fq2 FASTQ for second end. Used if BAM contains paired-end data. BAM should be sorted by query name is creating paired FASTQ. -tags Create FASTQ based on the mate info in the BAM R2 and Q2 tags.Tips: If you want to create a single, interleaved FASTQ file for paired-end data, you can just write both to /dev/stdout: bedtools bamtofastq -i x.bam -fq /dev/stdout -fq2 /dev/stdout > x.ilv.fq

Direct conversion to fastq for example:

bamToFastq -i unmapped.bam -fq unmapped.fastq

If you need to distinguish paired reads in bam files, you can:

bamToFastq -i unmapped.bam -fq unmapped Read1.fastq-fq2 unmapped Read2.fastq Read here, this article "how to convert fastq bam file" article has been introduced, want to master the knowledge points of this article also need to practice to understand, if you want to know more related content of the article, welcome to pay attention to the industry information channel.

Welcome to subscribe "Shulou Technology Information " to get latest news, interesting things and hot topics in the IT industry, and controls the hottest and latest Internet news, technology news and IT industry trends.