Hi all,
I have human paired end Miseq reads 2 by 50 (2x50). My insert size is 400 bp. I mapped the reads using bowtie 2 and I have positons for R1 and R2. I would like to extract unsequenced portion of each insert that is 300 bp between R1 and R2 read. Since I have genome fasta file I am guessing I can extract these reads by looking at the map positions.
I was wondering if anyone can recommend a tool or a Script, which I can modify if necessary. Thank you.
I have human paired end Miseq reads 2 by 50 (2x50). My insert size is 400 bp. I mapped the reads using bowtie 2 and I have positons for R1 and R2. I would like to extract unsequenced portion of each insert that is 300 bp between R1 and R2 read. Since I have genome fasta file I am guessing I can extract these reads by looking at the map positions.
I was wondering if anyone can recommend a tool or a Script, which I can modify if necessary. Thank you.
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