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Old 12-14-2012, 01:27 AM   #1
Carmen
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Default uniquely mapped reads

Hi,

Is there anyway to report ONLY uniquely mapped reads in bowtie sam output?
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Old 12-14-2012, 01:36 AM   #2
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Salut Carmen,

The method will depend on the version of bowtie you are using.

Are you using bowtie1 or bowtie2 ?

Mathieu
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Old 12-14-2012, 01:43 AM   #3
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My previous reply is inappropriate.

I posted a way to filter out multiple alignments from a SAM file, there : http://seqanswers.com/forums/showpos...45&postcount=6

Hope this will solve your problem,
Mathieu
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Old 12-14-2012, 01:58 AM   #4
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OK Mathieu,
I will try your way

Thanks for your replay
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Old 12-14-2012, 02:30 AM   #5
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Dear Mathieu,
I used the grep command for the XS tag but in the sam output of bowtie-0.12.7 (the version I used) there isn't this tag

Any other suggestion??

Carmen
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Old 12-14-2012, 03:27 AM   #6
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Well, it seems that my initial question (version of bowtie) was in the end appropriate.

In bowtie1, there is an option to report uniquely mapped reads only. From the bowtie1 manual :

Quote:
-m <int>

Suppress all alignments for a particular read or pair if more than <int> reportable alignments exist for it. Reportable alignments are those that would be reported given the -n, -v, -l, -e, -k, -a, --best, and --strata options. Default: no limit. Bowtie is designed to be very fast for small -m but bowtie can become significantly slower for larger values of -m. If you would like to use Bowtie for larger values of -k, consider building an index with a denser suffix-array sample, i.e. specify a smaller -o/--offrate when invoking bowtie-build for the relevant index (see the Performance tuning section for details).
Using -m 1 should fill your needs.

Mathieu
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Old 12-14-2012, 04:17 AM   #7
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I have already used the option -m 1
with this option the uniquely mapped reads are reported as number in the final report but in the final sam output file there are all the reads
I'm interested in a file in which are reported only the uniquely mapped reads

Carmen
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Old 12-14-2012, 04:51 AM   #8
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I would then switch to bowtie2 and use the method mentioned above.

Mathieu
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Old 12-14-2012, 05:01 AM   #9
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I will try two strategies
alignment with bowtie2
extraction of uniquely mapped reads from modified sam file with R

Carmen
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