Bowtie colorspace output has less NT than input reads

[SongLi]

Hi,

I am using bowtie for colorspace alignment. My data are 35nt reads (36nt if the first T is included). In the bowtie default output file, the decoded sequence space reads has only 33 NT displayed.

my command is:

bowtie -t -q -p 7 -C -n 3 -a --best MyGenomeSeq MyInput.fastq > MyOutput.aln &

Could anyone explain this?

Thanks,
Song Li

[zhidkov.ilia]

Hi SongLi,
one of the options in bowtie is trimimng bases from:
" -5/--trim5 <int>
Trim <int> bases from high-quality (left) end of each read before alignment (default: 0).

-3/--trim3 <int>
Trim <int> bases from low-quality (right) end of each read before alignment (default: 0). "

maybe you used it?

Ilia

[SongLi]

Hi,

Thank you for the reply. My command is included in my previous post. I did not use --trim unless it was default for colorspace alignment.

Best,
Song

Hi SongLi,
one of the options in bowtie is trimimng bases from:
" -5/--trim5 <int>
Trim <int> bases from high-quality (left) end of each read before alignment (default: 0).

-3/--trim3 <int>
Trim <int> bases from low-quality (right) end of each read before alignment (default: 0). "

maybe you used it?

Ilia

[zhidkov.ilia]

--trim option suppose to be 0 by default...

[zhidkov.ilia]

Ok, found this:
http://seqanswers.com/forums/showthread.php?t=7488

think it has the answer you looked for

PS
Learned something new myself, thank you

[SongLi]

Thank you for pointing out this link.

Ok, found this:
http://seqanswers.com/forums/showthread.php?t=7488

think it has the answer you looked for

PS
Learned something new myself, thank you