Hi Heng,
We ran BWA on simulated data of length 40/80nc which has max 2 errors in the prefix 20nc sequence and a total of 3 errors with the following parameters.
$HOME/bin64/bwa-0.5.4/bwa aln -i 0 -n $(($n+1)) -o $(($n+1)) -e $(($n+1)) -N -t 8 -l 20 -k 2
First we couldn't get any hits with $n=2 although the initial number of errors are supposed to <=3.
After running with $n=3 we got hits with edit distance >=4 when the alignment is done for the BWA output region, these turned out to be 3 edit distance hits. (See 2 examples below; I can provide more if necessary)
Is is due to a bug in the software?
>chr10|101603578|101603617|-|seqTGA_7580|39ins-30ins-39ins 5 5
chr10 -101603576 4
chr10 -101603575 4
chr20 +52093242 4
chr10 -101603577 4
chr10 -101603578 4
>chr10|102009379|102009418|+|seqTGT_3501|39ins-6ins-14ins 2 2
chr10 +102009377 4
chr10 +102009376 4
chr10|101603578|101603617|-|seqTGA_7580|39ins-30ins-39ins (43 nc) 43..1 chr10 101603578..101603617
chr10
errors: 3 orientation: -
ANTNCATCGTCANTCATCATCTGCATCATCATCATCATCATCA
| | |||||||| ||||||||||||||||||||||||||||||
A-T-CATCGTCA-TCATCATCTGCATCATCATCATCATCATCA
chr10|102009379|102009418|+|seqTGT_3501|39ins-6ins-14ins (43 nc) 1..43 chr10 102009379..102009418
chr10
errors: 3 orientation: +
GCTAAANCAAGTGTNGTACCGGGTTGTGGGAACGCAACGATNA
|||||| ||||||| |||||||||||||||||||||||||| |
GCTAAA-CAAGTGT-GTACCGGGTTGTGGGAACGCAACGAT-A
Biter Bilen
PhD Student
Zavolan Lab
Biozentrum
Klingelbergstrasse 50
4056 Basel Switzerland
We ran BWA on simulated data of length 40/80nc which has max 2 errors in the prefix 20nc sequence and a total of 3 errors with the following parameters.
$HOME/bin64/bwa-0.5.4/bwa aln -i 0 -n $(($n+1)) -o $(($n+1)) -e $(($n+1)) -N -t 8 -l 20 -k 2
First we couldn't get any hits with $n=2 although the initial number of errors are supposed to <=3.
After running with $n=3 we got hits with edit distance >=4 when the alignment is done for the BWA output region, these turned out to be 3 edit distance hits. (See 2 examples below; I can provide more if necessary)
Is is due to a bug in the software?
>chr10|101603578|101603617|-|seqTGA_7580|39ins-30ins-39ins 5 5
chr10 -101603576 4
chr10 -101603575 4
chr20 +52093242 4
chr10 -101603577 4
chr10 -101603578 4
>chr10|102009379|102009418|+|seqTGT_3501|39ins-6ins-14ins 2 2
chr10 +102009377 4
chr10 +102009376 4
chr10|101603578|101603617|-|seqTGA_7580|39ins-30ins-39ins (43 nc) 43..1 chr10 101603578..101603617
chr10
errors: 3 orientation: -
ANTNCATCGTCANTCATCATCTGCATCATCATCATCATCATCA
| | |||||||| ||||||||||||||||||||||||||||||
A-T-CATCGTCA-TCATCATCTGCATCATCATCATCATCATCA
chr10|102009379|102009418|+|seqTGT_3501|39ins-6ins-14ins (43 nc) 1..43 chr10 102009379..102009418
chr10
errors: 3 orientation: +
GCTAAANCAAGTGTNGTACCGGGTTGTGGGAACGCAACGATNA
|||||| ||||||| |||||||||||||||||||||||||| |
GCTAAA-CAAGTGT-GTACCGGGTTGTGGGAACGCAACGAT-A
Biter Bilen
PhD Student
Zavolan Lab
Biozentrum
Klingelbergstrasse 50
4056 Basel Switzerland
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