To anyone who may have dealt with Illumina MiSeq paired end reads: what are the best programs/scripts to use when merging the R1 and R2 (forward and reverse) read pairs into extended consensus..es (is there a plural for 'consensus')? I've tried four different program suites (pRESTO, flash, fastq-join, seqimp) and they all miss many, many read pairs that obviously overlap, sometimes even better than the reads that were merged. I sequenced adapter ligated microRNAs with barcodes. The MiSeq was readily able to identify the barcodes and eliminated most of the adapter sequence, and the read qualities are generally quite good, but I'm disturbed that my mergers aren't coming out as they should. I don't want to just take one of the files and accidentally identify a microRNA in a read that actually might have been a tRNA, or some other sequence type that I would have been able to eliminate by discovering that it was in fact a longer sequence after a proper read merger.
Any advice would be most appreciated!
My apologies if this question has been asked previously (tried searching, but nothing came up using various keyword combinations).
Any advice would be most appreciated!
My apologies if this question has been asked previously (tried searching, but nothing came up using various keyword combinations).
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