filter high quality solexa reads

[strob]

Dear all,

I just received data from illumina (100nt reads).
The file is named: mRNAseq_7_sequence.txt
and it looks like this:

HWUSI-EAS1999_9996:7:1:2:618#0/1:NATGTTTTTTTTTTTCAAGAACGAAAGTTNGGGGCTCGAAGACGATCAGATACCGAGAAAAAAAAAAAATCGTATGCCGTCTTCTGCTTGAAAAAAAAAAA:FNNNMWWTTYeeeeeeeeeeeeeeeRRTTEVVUUUeeeeeeeeeeeeeeeeeeeeeeee\eeeeeee[ee^\\[[\^\\\\^ZY[eee[eeeeeeBBBBB
HWUSI-EAS1999_9996:7:1:2:1071#0/1:GACGACTTCTCCGGGGGGGAAATGATAAGNTTCAGTGGACTTCCCCCCCCCCCGCGGGCAGCGAAAAAAAAAAAAAAACCGAGATCGGAAGAGCTCGTATG:EHHHHMMJJJeeeeeeeeee\eeeeKKJJEPNNPP\^^Y\^\^^Yeeeee\[\\[ee[e[\\^[\eeeeeBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
HWUSI-EAS1999_9996:7:1:2:264#0/1:NGGCCATCAGTAGGGTAAAAAAAAAAAAANTCACGACGGTCTAAACCCAGCTTTTTTTTTTGAAGAGCTCGTATGCCCCCCCCCCCTTGAAAAAAAAAAA:FTVVV^^Y^^eeeeeeeeeeeeeee^^^ZFRRVROeeeeeeeeeeeeeeeeee[eeeeeeeeeeeeeeeeee\eeee[eeeeeee\e[[e\[^BBBBBBB


I have been searching all over the net, but there is too much info, so here is my question: how can I filter for high quality reads? I want to filter for reads which have or an average quality above a certain threshold or have a certain number of bases below a certain threshold. Is there a way to do this?

Next I want to convert this to 1. solexa fastq ; 2. normal fastq; ...

As I want to use this data in GALAXY, I should also be able to upload it there.

Any help is more than welcome

Steven

[svl]

Next I want to convert this to 1. solexa fastq ; 2. normal fastq

Normally the _sequence.txt files are in fastq format...
-----
@GAII:6:1:50:677#0/1
ATGCTT etc
+GAII:6:1:50:677#0/1
Z]^_^^ etc
-----
...so why didn't they just give you those?

Anyway, to get fastq back, you would have to split every line in your file into four parts and print back
@header
sequence
+header
quality-values

And when you have fastq, you can indeed use galaxy to trim your reads based on quality

-svl