Lishiyong,

You should not convert colorspace to base space prior to aligning reads. The reason for this is that if there is an error in one of the color calls, it will effect all the downstream color calls.

Instead, you should use an aligner that will do the assembly in color-space instead. I know there are a few out there, but don't know them off the top of my head.

Ryan

On 3/27/11 11:35 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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