Question

Extract R1 and R2 from sam file generated by bowtie2

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2.5 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

ADD COMMENT • link updated 2.5 years ago by iraun 6.2k • written 2.5 years ago by Ahmad ▴ 10

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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?

ADD REPLY • link 2.5 years ago by iraun 6.2k

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

ADD REPLY • link 2.5 years ago by Ahmad ▴ 10

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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.

ADD REPLY • link 2.5 years ago by iraun 6.2k

score 0 · Answer 1 · 2022-06-06

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2.5 years ago

kanika.151 ▴ 160

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

ADD COMMENT • link 2.5 years ago by kanika.151 ▴ 160