I have a couple of doubts about Fastq joiner:
1) on the Fastq joiner instructions I see that the program will join the paired ends, but will exclude sequences that have lost their pair during quality check. Is there a way of keeping these lone sequences rather than ditching them?
2) the sequences joining scheme seems to simply concatenate /1 and /2 seqs as they are: shouldn't /2 seqs be reverted? shouldn't they be separated by an N in the middle in the final output?
@HWI-EAS91_1_30788AAXX:7:21:1542:1758/1 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATC +HWI-EAS91_1_30788AAXX:7:21:1542:1758/1 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh
@HWI-EAS91_1_30788AAXX:7:21:1542:1758/2 GCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA +HWI-EAS91_1_30788AAXX:7:21:1542:1758/2 hhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
A multiple-fastq file, for example:
@HWI-EAS91_1_30788AAXX:7:21:1542:1758 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATCGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA +HWI-EAS91_1_30788AAXX:7:21:1542:1758
Thank a lot by the help!