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Hi,
Is there anyway to report ONLY uniquely mapped reads in bowtie sam output?
Is there anyway to report ONLY uniquely mapped reads in bowtie sam output?
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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 -
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,
MathieuComment
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OK Mathieu,
I will try your way
Thanks for your replayComment
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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??
CarmenComment
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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 :
Using -m 1 should fill your needs.-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).
MathieuComment
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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
CarmenComment
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I would then switch to bowtie2 and use the method mentioned above.
MathieuComment
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I will try two strategies
alignment with bowtie2
extraction of uniquely mapped reads from modified sam file with R
CarmenComment
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
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...06-02-2026, 10:05 AM
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