Removing unpaired read from HiSeq paired end fastq file

[SeqTrbl]

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.

[GenoMax]

See: http://www.biostars.org/p/6925/ Eric Normandeau's script should do what you need.

Some additional options discussed in a previous thread: http://seqanswers.com/forums/showthread.php?t=17974

[lovenlong]

Hi,
Sickle would perfectly work for you.
I did preprocessing by combining scythe (trimming adaptors), Fastx_tools and Synche (pe option).

Best regards

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.