a question about bowtie (--best --strata)

kaixinsjtu · 11-15-2012, 06:57 AM

bowtie -a --best --strata -p 6 /bowtie/indexes/hg18 -c AAAAACGGACCAAGGAGTCTA
0 - chr5 163808619 TAGACTCCTTGGTCCGTTTTT IIIIIIIIIIIIIIIIIIIII 1 6:A>C,13:T>C
0 + chr3 15801900 AAAAACGGACCAAGGAGTCTA IIIIIIIIIIIIIIIIIIIII 1 16:C>G,18:T>C
# reads processed: 1
# reads with at least one reported alignment: 1 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 2 alignments to 1 output stream(s)

$ bowtie -a -p 6 /bowtie/indexes/hg18 -c AAAAACGGACCAAGGAGTCTA
0 + chr3 15801900 AAAAACGGACCAAGGAGTCTA IIIIIIIIIIIIIIIIIIIII 0 16:C>G,18:T>C
# reads processed: 1
# reads with at least one reported alignment: 1 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 1 alignments to 1 output stream(s)

WHY? why --best --strata gives an extra alignment??? I got totally confused... Anyone help me out?

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11-15-2012, 06:57 AM	#1
kaixinsjtu Junior Member Location: HOUSTON Join Date: Nov 2008 Posts: 9	a question about bowtie (--best --strata) bowtie -a --best --strata -p 6 /bowtie/indexes/hg18 -c AAAAACGGACCAAGGAGTCTA 0 - chr5 163808619 TAGACTCCTTGGTCCGTTTTT IIIIIIIIIIIIIIIIIIIII 1 6:A>C,13:T>C 0 + chr3 15801900 AAAAACGGACCAAGGAGTCTA IIIIIIIIIIIIIIIIIIIII 1 16:C>G,18:T>C # reads processed: 1 # reads with at least one reported alignment: 1 (100.00%) # reads that failed to align: 0 (0.00%) Reported 2 alignments to 1 output stream(s) $ bowtie -a -p 6 /bowtie/indexes/hg18 -c AAAAACGGACCAAGGAGTCTA 0 + chr3 15801900 AAAAACGGACCAAGGAGTCTA IIIIIIIIIIIIIIIIIIIII 0 16:C>G,18:T>C # reads processed: 1 # reads with at least one reported alignment: 1 (100.00%) # reads that failed to align: 0 (0.00%) Reported 1 alignments to 1 output stream(s) WHY? why --best --strata gives an extra alignment??? I got totally confused... Anyone help me out?