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Old 12-14-2009, 07:18 AM   #1
fargo
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Default bowtie output

Hi, I am a newbie in bioinformatics. I am trying to use bowtie to map a set of sequences. Here is the result I have got.

Time loading forward index: 00:00:12
Time loading mirror index: 00:00:13
Seeded quality full-index search: 07:49:33
# reads processed: 440372
# reads with at least one reported alignment: 193962 (44.05%)
# reads that failed to align: 246410 (55.95%)
Reported 1903683060 alignments to 1 output stream(s)
Time searching: 07:49:58
Overall time: 07:49:59

Is there a way to display more information than it is above? For example, the percentage of reads that are uniquely mapped. Thanks.
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Old 12-14-2009, 11:03 AM   #2
DrD2009
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Hi, I'm also new, but I think I can help you out.

In the command line when you told bowtie to align your query sequence file(s) did you specify a directory for the output or did you just name it?

If you specified a directory you'll find the txt file in that directory and you can open it up and view it using your favorite text editor. If you have problems viewing it you can upload the file to Galaxy (http://main.g2.bx.psu.edu/) and view it there. I know sometimes I'll try to open the bowtie outputs in Windows and they won't open.

Example: bowtie <options> index query /../.../..../..../file.map

If you didn't specify a directory for the bowtie output then you will find it in your bowtie folder.

Example: bowtie <options> index query file.map


Hope this helps.

-Brandon
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Old 12-15-2009, 07:15 PM   #3
fargo
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Thanks for your reply. I am not sure about the map file. Is that the mapping output?

Here is the command I have used.

bowtie mm9 -r -n 1 -l 36 -a sequences-input -t > mapping

The mapping result is stored in the mapping.


But these info are displayed on the terminal.

Time loading forward index: 00:00:12
Time loading mirror index: 00:00:13
Seeded quality full-index search: 07:49:33
# reads processed: 440372
# reads with at least one reported alignment: 193962 (44.05%)
# reads that failed to align: 246410 (55.95%)
Reported 1903683060 alignments to 1 output stream(s)
Time searching: 07:49:58
Overall time: 07:49:59
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Old 12-15-2009, 07:48 PM   #4
DrD2009
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I'm not sure if there is a way to produce a file with an outline of different aspects of your alignment, but to address your unique reads mapped question you could try the following parameters:

Use "-k 1" (which is a Bowtie default) instead of "-a"
This will cause Bowtie to report the first valid alignment it encounters. I'm going to assume all others that align to the same position will not be added to the alignment file and thus you'd be able to view the percentage and number of "reads with at least one reported alignment" using the -t option.

In theory I think the above solution will work for the query you had. I would definitely consult the Bowtie manual, it is a wealth of information.

-Brandon
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Old 02-19-2010, 11:57 PM   #5
ECHo
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Well, I think the command would be as follows:
bowtie mm9 -r -n 1 -l 36 -a sequences-input -t 2> result

Maybe you should replace > with 2>
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