I have been having some issues doing a paired end analysis simply due to the way I am processing things.
I currently use custom illumina adaptors that have in-line barcodes i.e. the first 7 nucleotides sequenced in the run (either 1st read or paired end read)
Briefly, I have designed a customized protocol which ligates a different barcode to each end of an insert. i.e. in a paired end sequence the two barcodes will be different at either end.
After de-barcoding these split as different files. Even though the files can be combined after debarcoding there are still issues.
Since the sequence of a barcode may not be distinguished by fastx BC splitter as a case (read) to case (read) basis, it will definitely mess up the order of the reads, such that read1 does not align with its mate in the read2 fastq file.
I still want to conduct a paired end analysis and was wondering if there is a way of re pairing the reads after de-barcoding.
I currently use custom illumina adaptors that have in-line barcodes i.e. the first 7 nucleotides sequenced in the run (either 1st read or paired end read)
Briefly, I have designed a customized protocol which ligates a different barcode to each end of an insert. i.e. in a paired end sequence the two barcodes will be different at either end.
After de-barcoding these split as different files. Even though the files can be combined after debarcoding there are still issues.
Since the sequence of a barcode may not be distinguished by fastx BC splitter as a case (read) to case (read) basis, it will definitely mess up the order of the reads, such that read1 does not align with its mate in the read2 fastq file.
I still want to conduct a paired end analysis and was wondering if there is a way of re pairing the reads after de-barcoding.
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