Hello Lishiyong,

Just to confirm, the conversion was performed at Galaxy main using "NGS: QC and manipulation -> Convert SOLiD output to fastq"? With the option "double encode = yes"? If so, the output appears to be correct.

quote from tool help:

"Double encode? - converts color calls (0123.) to pseudo-nucleotides (ACGTN). Not necessary for bowtie. Required for BWA."

Please let us know if we can help more,

Best,

Jen
Galaxy team

On 3/27/11 8:35 PM, lishiyong wrote:
Hello!

I convert SOLiD csfasta- and qual-files to fastq-files ,I want to use
the fastq-files to do denovo with *SOAPdenovo*.because the SOLiD de novo
accessory tools Require large memory .But ,I find that there're some
question for the converting .

for example:

T02023221102101032002002030011232121133222233311200 ——>
AGAGTGGCCAGCACATGAAGAAGATAACCGTGCGCCTTGGGGTTTCCGAA
But I think it should to be
TCCTAGACAAGTTGGCTTTCCCTTAAACAGCTGACATAGAGATATGTCCC Who knows the reason
about this.
2011-03-28
------------------------------------------------------------------------
lishiyong



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