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Old 06-29-2010, 03:58 AM   #1
PHSchi
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Default qseq.txt to fq reloaded

Hi! I am trying to convert Illumina qseq.txt looking like this
HWUSI-EAS488 1 1 54 0 973 0 1 .......................................................................................................... BBBBBBB
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB 0
HWUSI-EAS488 1 1 54 0 1367 0 1 ......

to fq using the qseq2fastq.pl posted here by Xi Wang.
However, the resulting fastq (or fq) files come out like this
@HWUSI-EAS488:1:1:0:1398#0/2
..........................................................................................................
+
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@HWUSI-EAS488:1:1:0:167#0/2
.........................................................................................................

,which for me seems to hold no sequence information, as I expected something like this:
@1:2:12:1486
TATAACATGGGANATGTTATAGTATNNNNNNNNTTAAAACATTNNANNNGNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+1:2:12:1486
aaaaa`a_aa[ZDZ`a^`_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@1:2:12:2015
CCAACCTGCTTTNGAGGCATAGACANNNNNNNNCTCATGTACANNTNNNANNCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+1:2:12:2015
`bba_aababaZDW^`abbbbbbbYDDDDDDDD\aaabbBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
.
Or am I actually mixing up different formats?
Thanks!
P
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Old 06-29-2010, 05:27 AM   #2
PHSchi
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Ah, okay, should do more wikipedia before posting...
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Old 06-29-2010, 08:07 PM   #3
Daniel Su
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Yes, your descriptions of the two format are right. However, the qseq-format sequence you posted does not have signals.(that's .................................................. .................................................. ......)

You may try other sequences (in your qseq.txt).
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