Extract R1 and R2 from sam file generated by bowtie2
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A combination of two tools can be used to achieve this: gatk PrintReads and picard RevertSam.
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kanika.151
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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?
yes, I need spilt the sam file into R1 and R2 to make re- alignment
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 asbbmap.