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

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

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