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Old 01-19-2011, 10:31 AM   #1
SongLi
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Default Bowtie colorspace output has less NT than input reads

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
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Old 01-19-2011, 10:57 AM   #2
zhidkov.ilia
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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
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Old 01-19-2011, 11:02 AM   #3
SongLi
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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

Quote:
Originally Posted by zhidkov.ilia View Post
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
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Old 01-19-2011, 11:55 AM   #4
zhidkov.ilia
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--trim option suppose to be 0 by default...
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Old 01-19-2011, 12:21 PM   #5
zhidkov.ilia
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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
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Old 01-20-2011, 08:39 AM   #6
SongLi
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Thank you for pointing out this link.



Quote:
Originally Posted by zhidkov.ilia View Post
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
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