QuasR::qAlign: how to specify maximum allowed number of mismatches and output all alignments
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Julie Zhu ♦ 4.3k
@julie-zhu-3596
Last seen 4 days ago
United States

Dear QuasR developers,

I would like to use the qAlign function in QuasR. However, I do not see any parameters for specifying the number of mismatches allowed (-v parameter in bowtie) or the number of alignments (-k parameter in bowtie) to output for a multi-mapping read. According to the help menu, a single alignment is randomly selected in case of a multi-mapping read.

Could you please let me know whether it is possible to specify v and k in qAlign? Would you suggest I should use Rbowtie::bowtie instead.

Thanks!

Best regards, Julie

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@hotz-hans-rudolf-3951
Last seen 4 months ago
Switzerland

Hi Julie

There is the 'alignmentParameter' argument. You can use it to provide command line parameters to be used for the aligner. The defaults will then be overruled. But (quoting the QuasR documentation): "Please use with caution; some alignment parameters may break assumptions made by QuasR. "

Regards, Hans-Rudofl

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@michael-stadler-5887
Last seen 7 days ago
Switzerland

Just to add to Hans-Rudolf's reply:

The default parameters that qAlign uses are: -m X --best --strata

where X is the value passed to qAlign(..., maxHits = X)

You could add -v using for example (please note that this will ignore the base qualities of your reads): qAlign(..., alignmentParameter = "-m 10 --best --strata -v 2")

Adding -k Y with a value of Y greater than one has to be used with caution (it falls under the "breaks assumptions made by QuasR" category mentioned by Hans-Rudolf). For example, qCount may count your read more than once (redundant use of information), and alignmentStats my report more alignments than the total number of reads sequenced.

Best regards, Michael

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Hi Michael,

Thank you very much for the detailed information! It’s very helpful!

Best regards,

Julie

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