Extract R1 and R2 from sam file generated by bowtie2
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2.4 years ago
Ahmad ▴ 10

Hi every one

How to extract R1 and R2 from sam file generated by bowtie2 ?

sam bowtie2 samtools bam • 1.1k views
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What do you mean by "extract R1 and R2"? Do you want to extract the paired mapped reads? In fasta or fastq format?

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yes, I need spilt the sam file into R1 and R2 to make re- alignment

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I recommend you to search a bit through biostars questions, since it has been asked before (Sam to fastq). There are many tools that can do this job, personally I use Picard SamToFastq ( see here), but there are many nice other alternatives such as bbmap.

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2.4 years ago
kanika.151 ▴ 150

A combination of two tools can be used to achieve this: gatk PrintReads and picard RevertSam.

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