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Old 08-11-2010, 02:08 PM   #21
Lee Sam
Location: Ann Arbor, MI

Join Date: Oct 2008
Posts: 57

Originally Posted by fkrueger View Post
I was talking about the -e ceiling (not the -n ceiling which applies for the seed length, which can be anything between 0 and 3), which is defined as follows:

-e/--maqerr <int>
Maximum permitted total of quality values at all mismatched read positions throughout the entire alignment, not just in the "seed". The default is 70. Like Maq, bowtie rounds quality values to the nearest 10 and saturates at 30; rounding can be disabled with --nomaqround.

This means that each mismatch in a fastA file counts as 30, i.e. 3 mismatches (even if it is quite close to the 3' end of the sequence) willexceed the default value of 70 and cause the sequence to be removed (and scored as not aligned).
I see the manual changed a little since 0.10.0 (last version where I regularly read the manual), which read:

-e/--maqerr <int> The maximum permitted total of quality values at
mismatched read positions. This total is also
called the "quality-weighted hamming distance" or
"Q-distance." This is analogous to the -e option
for "maq map". The default is 70. Note that,
like Maq, Bowtie rounds quality values to the
nearest 10 and saturates at 30.
I was confused in my understanding of how the -e parameter works then. I had been under the impression that the totals were only within the seed region. I stand corrected.
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Old 03-05-2011, 04:04 PM   #22
Location: Brazil

Join Date: Oct 2010
Posts: 13


I did the transcriptome SOLID, but reads not fully aligned, I'm losing 16 million of the data. what happened? where can I find? which software to use? I used the Bioscope. Can I use phred filter??
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