uniquely mapped reads

Carmen · 12-14-2012, 02:27 AM

Hi,

Is there anyway to report ONLY uniquely mapped reads in bowtie sam output?

MGineste · 12-14-2012, 02:36 AM

Salut Carmen,

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

Are you using bowtie1 or bowtie2 ?

Mathieu

MGineste · 12-14-2012, 02:43 AM

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

Carmen · 12-14-2012, 02:58 AM

OK Mathieu,
I will try your way

Thanks for your replay

Carmen · 12-14-2012, 03:30 AM

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

MGineste · 12-14-2012, 04:27 AM

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

Carmen · 12-14-2012, 05:17 AM

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

MGineste · 12-14-2012, 05:51 AM

I would then switch to bowtie2 and use the method mentioned above.

Mathieu

Carmen · 12-14-2012, 06:01 AM

I will try two strategies
alignment with bowtie2
extraction of uniquely mapped reads from modified sam file with R

Carmen

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12-14-2012, 02:27 AM	#1
Carmen Member Location: Italy Join Date: Aug 2012 Posts: 10	uniquely mapped reads Hi, Is there anyway to report ONLY uniquely mapped reads in bowtie sam output?

12-14-2012, 02:36 AM	#2
MGineste Member Location: Montpellier, France Join Date: Feb 2011 Posts: 21	Salut Carmen, The method will depend on the version of bowtie you are using. Are you using bowtie1 or bowtie2 ? Mathieu

12-14-2012, 02:43 AM	#3
MGineste Member Location: Montpellier, France Join Date: Feb 2011 Posts: 21	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

12-14-2012, 02:58 AM	#4
Carmen Member Location: Italy Join Date: Aug 2012 Posts: 10	OK Mathieu, I will try your way Thanks for your replay

12-14-2012, 03:30 AM	#5
Carmen Member Location: Italy Join Date: Aug 2012 Posts: 10	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

12-14-2012, 05:17 AM	#7
Carmen Member Location: Italy Join Date: Aug 2012 Posts: 10	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

12-14-2012, 05:51 AM	#8
MGineste Member Location: Montpellier, France Join Date: Feb 2011 Posts: 21	I would then switch to bowtie2 and use the method mentioned above. Mathieu

12-14-2012, 06:01 AM	#9
Carmen Member Location: Italy Join Date: Aug 2012 Posts: 10	I will try two strategies alignment with bowtie2 extraction of uniquely mapped reads from modified sam file with R Carmen