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Old 08-01-2009, 06:11 AM   #1
Ally
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Question bowtie output file format

Dear all,

I need to analysis some raw data using bowtie, then transfer them to cisgenome to make a deeper analysis. Now I get the results from bowtie, just like this7 out of all)
44 + 6 67542638 AGGGGATAGATACCCCATATACCCTGGTGCAATTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 0
45 + 16 19579916 AGCCAAGATCATGCCACTGCACTCCAGCCTGGGCAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 675
46 + 12 48595908 AATGCAAATCAAAACCACAATGAGCTACCATCTCAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 19
47 + 19 17650887 AAACACACACAAGGTGTTACTAAGCATTACCCGTCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 0
48 + 4 155793608 AACCAATCCCAGTTACCAGGAGATGCCAAATGCTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 0
49 - 4 108634190 ATAGCTATTAAGGGAAACAGACGATAATCCAACTGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 0 14:T>C
29 - 1 91611574 TTTCCTTGTATAAACAAGCAAATATTTATACTGGTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 6 3:A>G

could some tell me the meaning of last 3 columns? I cannot understand....
And do some know what I can do next to analysis them using cisgenome?

Thanks in advance!!
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Old 08-01-2009, 08:19 AM   #2
Ben Langmead
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Hi Ally,

Quote:
Originally Posted by Ally View Post
could some tell me the meaning of last 3 columns? I cannot understand....
Check out the output section of the Bowtie manual.

Thanks,
Ben
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Old 08-01-2009, 06:33 PM   #3
Ally
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Thank you! I haven't noticed it before....
but there comes another question, when I use the package in "Bowtie_indexes" named "human_crossbow", I get the result above. Yesterday I tried another package "h_sapiens.ebwt", and got the following results:
0 + gi|88998470|ref|NT_025741.14|Hs6_25897 33945950 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 15627
1 - gi|29791548|ref|NT_006238.10|Hs4_6395 3719515 ATGGTTTGGCTCTACGTCCCCACCCAAATCTCATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 0
2 - gi|51465008|ref|NT_006713.14|Hs5_6870 16860071 GAAAAAATCTGAAGATGCACGTACCAGATGGTAATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 0 17:T>A

I wonder why this happen?? Is there something wrong ? What's the difference between the two package??
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Old 08-01-2009, 07:16 PM   #4
Ben Langmead
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Hi Ally,

The official indexes are linked to from the sidebar of the Bowtie page. "human_crossbow" is an old package. If you're doing alignment to human, use either the human contigs ("h_sapiens") or the human assembly ("h_sapiens_asm") index linked to from the main page.

Thanks,
Ben
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Old 08-01-2009, 08:40 PM   #5
Ally
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Thank you very much!!!
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