Hi,
I try to split fastq file containing multiple samples (illumina paired end, miseq run). These are not general barcodes read directly on the machine - they are simply embedded within the read (forward only, first 6bp, reverse has no index).
Tried to use FASTX toolkit but there is no way to use it with paired end.
Managed to successfuly split the read1 using FASTX but how to match read2 reads ?
Is there any tool to directly work on PE reads?
Thanks in advance!
b
I try to split fastq file containing multiple samples (illumina paired end, miseq run). These are not general barcodes read directly on the machine - they are simply embedded within the read (forward only, first 6bp, reverse has no index).
Tried to use FASTX toolkit but there is no way to use it with paired end.
Managed to successfuly split the read1 using FASTX but how to match read2 reads ?
Is there any tool to directly work on PE reads?
Thanks in advance!
b
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