Quality Control question

[dicty]

Hi,

I used SolexaQA for quality control and filtering, then I used Bowtie to align the reads before trimmed and after trimmed respectively. Below are the result summaries. Why more short reads are aligned after the data was trimmed? Is it because a lot of trimmed reads are aligned because the very short 1-4 nt trimmed reads are aligned to the genome sequence?

before trimmed:
# reads processed: 20669764
# reads with at least one reported alignment: 11454909 (55.42%)
# reads that failed to align: 9214855 (44.58%)
Reported 11454909 alignments to 1 output stream(s)

trimmed data:
# reads processed: 20669764
# reads with at least one reported alignment: 14205865 (68.73%)
# reads that failed to align: 6463899 (31.27%)
Reported 14205865 alignments to 1 output stream(s)

Thanks,

Dicty

[csoong]

could be a number of reasons. most likely you trimmed off the reads that had bad qualities and affected proper alignments (like going over the n value stuff like that). Im not familiar with SolexaQA at all so I could be totally off point.