[mira_talk] New Solexa file format not supported by mira?
- From: Nicolas Balcazar <balcazar@xxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sat, 13 Aug 2011 15:59:59 +0200
Hi,
I encounter the problem that mira doesnt seem to recognize my solexa reads
as paired end. (denovo assembly)
I have two files (which i merged together into one, since it looks like mira
just accepts ONE input file even though being paired-end data) with the
folowing format:
> head myData_in.solexa.fastq
@HWI-H155:68:81MMAABXX:1:1101:1351:2105 1:N:0:GCCAAT
TAAGCGAGCAAAATAGTGTCAGAGGTCAGGAGAGAAGGAAACTCACCTCTTGGCTGGAATCTCAATCTTATAAATCACTTCCTCAGAACCAGCGGCCTCTT
+
@@CDFDBDHHHFH<FF<E3CFE<FF?EBGGGGGI<FHHIGBFBGHII).)1/...5;=A@GCHAEHEC
;;77;?###########################
@HWI-H155:68:81MMAABXX:1:1101:1493:2111 2:N:0:GCCAAT
AAAGCAAAACTTGAGCTGCGAGCATTCCTTGAACCTTTGCATCCACGACTTTGAGGAAGAGGAACGAAGCTGCTGTGCGTAAGAGCCGTGGCGAAAATTGT
+
??;D+AADHHF4A?:A<EGE@E:?E4CFABGGGDC;F*?B*9?*?3?D'-;7B;;7@C6
=A########################################
here the read pairs are denoted by the "1" and "2" before ":N:0:GCCAAT"
I know that the previous version was with "/1" and "/2". Can this be the
problem?
Do i have to change all @headers now??
details:
http://en.wikipedia.org/wiki/FASTQ_format#Illumina_sequence_identifiers
Thanks, Nicolas
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