Question

GenomicAlignments and mapping CIGAR coordinates

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stephen.rudd • 0

@stephenrudd-21782

Last seen 5.2 years ago

I am using the GenomicAlignments package for a bioinformatics tutorial that I am preparing. I would like to map coordinates between query reads and reference genome on the basis of the reported CIGAR string.

GenomicAlignments offers the documentation for e.g. queryLoc2refLoc - but the method (as of version 1.21.7) appears not to have been implemented with a rather brutal stop("NOT IMPLEMENTED YET, SORRY!")

Can anyone recommend any other R packages that might help here - the closest method that I have been able to find if the PERL Bio::Cigar (https://github.com/MullinsLab/Bio-Cigar/blob/master/lib/Bio/Cigar.pm)

Thanks

Stephen

cigar not-implemented-yet • 1.5k views

ADD COMMENT • link updated 5.2 years ago by Hervé Pagès 16k • written 5.2 years ago by stephen.rudd • 0

score 1 · Answer 1 · 2019-10-25

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Hervé Pagès 16k

@herve-pages-1542

Last seen 13 hours ago

Seattle, WA, United States

Hi,

Take a look at ?mapToAlignments in the GenomicAlignments package.

The reason queryLoc2refLoc() never got implemented is because (1) it's a low-level utility not really intended to be used directly by the end user, and (2) the purpose of the utility was to support higher level (i.e. user facing) mapping functions like mapToAlignments() and family but these functions were finally implemented without the need for queryLoc2refLoc().

Hope this helps,

H.

ADD COMMENT • link 5.2 years ago Hervé Pagès 16k

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I've tried to make the error message more useful in GenomicAlignments 1.21.8:

> queryLoc2refLoc(11:13, "55M")
Error in queryLoc2refLoc(11:13, "55M") : 
  Not implemented yet, sorry! Please use mapToAlignments() and family if
  you need to map coordinates between query reads and reference genome on
  the basis of the reported CIGAR. See '?mapToAlignments'

Best,

H.

ADD REPLY • link 5.2 years ago Hervé Pagès 16k