Hi
I have a modified sample prep protocol for hiseq paired end run, for which I need to do some quality checking for both read1 and read2 independent of each other. During this some reads missed their mate from both read1 and read2 fastq file. Now I have few reads in read1 which mates in read2 are deleted and viceversa. Now, is there any tool by which I can remove the unpaired reads from both read1 and read2 file. I tried writing code; but since these are hiseq files its taking a very long time.
I have a modified sample prep protocol for hiseq paired end run, for which I need to do some quality checking for both read1 and read2 independent of each other. During this some reads missed their mate from both read1 and read2 fastq file. Now I have few reads in read1 which mates in read2 are deleted and viceversa. Now, is there any tool by which I can remove the unpaired reads from both read1 and read2 file. I tried writing code; but since these are hiseq files its taking a very long time.
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