Hello,
I'm trying to use BOWTIE to find less aligned sequences to the mouse genome, and even better sequence that has 0 % matching.
Is it possible via Bowtie?
More over, I have the following read 'GAGCAAACAGAAAAACCAACCCCGGCTGATCGGAAACAGGCA' which matches 100% to chr12 in mm10 (mouse) genome. For this match (see below the results) I got maximum score.
I don't understand why if I change 3 bases randomly in the middle, or add 4 random bases at 3'/5' it does not align the read anymore, and don't display score overthought there is still big similarity. Don't understand why it misses a short alignments (10-30 bases) in a 100 bases read for example.
The command I used was:
CL:"C:\bowtie2\bowtie2-align-s.exe --wrapper basic-0 --local -N 1 -L 2 --gbar 100 --ma 2 --mp 0,0 --score-min L,0,0 -x D:/Augmanity/index/mm10 -f C:/bowtie2/reads/100LengthReads.fa --passthrough"
Attached the results:
Mouse-exact_seq 0 chr12 56691388 44 42M * 0 0 GAGCAAACAGAAAAACCAACCCCGGCTGATCGGAAACAGGCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:84 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:42 YT:Z:UU
Mouse-3_add_bases 4 * 0 0 * * 0 0 GAGCAAACAGAAAAACCAACCCCGGCTGATCGGAAACAGGCATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UU
Mouse-4-mismatches 4 * 0 0 * * 0 0 GAGCAAACAGAAAAACCAAAAAAGGCTGATCGGAAACAGGCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UU
I will appreciate any help. Thank you.
Anastasia
I'm trying to use BOWTIE to find less aligned sequences to the mouse genome, and even better sequence that has 0 % matching.
Is it possible via Bowtie?
More over, I have the following read 'GAGCAAACAGAAAAACCAACCCCGGCTGATCGGAAACAGGCA' which matches 100% to chr12 in mm10 (mouse) genome. For this match (see below the results) I got maximum score.
I don't understand why if I change 3 bases randomly in the middle, or add 4 random bases at 3'/5' it does not align the read anymore, and don't display score overthought there is still big similarity. Don't understand why it misses a short alignments (10-30 bases) in a 100 bases read for example.
The command I used was:
CL:"C:\bowtie2\bowtie2-align-s.exe --wrapper basic-0 --local -N 1 -L 2 --gbar 100 --ma 2 --mp 0,0 --score-min L,0,0 -x D:/Augmanity/index/mm10 -f C:/bowtie2/reads/100LengthReads.fa --passthrough"
Attached the results:
Mouse-exact_seq 0 chr12 56691388 44 42M * 0 0 GAGCAAACAGAAAAACCAACCCCGGCTGATCGGAAACAGGCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:84 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:42 YT:Z:UU
Mouse-3_add_bases 4 * 0 0 * * 0 0 GAGCAAACAGAAAAACCAACCCCGGCTGATCGGAAACAGGCATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UU
Mouse-4-mismatches 4 * 0 0 * * 0 0 GAGCAAACAGAAAAACCAAAAAAGGCTGATCGGAAACAGGCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UU
I will appreciate any help. Thank you.
Anastasia
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