How to find the end position of a read?
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Frocha ▴ 10
@frocha-12039
Last seen 3.4 years ago

I have a .sam file (for single-end reads) and I wish to find the end position of each read. I noticed that I can do that using Rsamtools if the file is a .bam file. However, I wish to do it directly on .sam file. How should I do? (using cigar value?)

Thanks!

 

rsamtools alignment cigar • 874 views
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@martin-morgan-1513
Last seen 9 weeks ago
United States

You could read the start and cigar from the SAM file using standard R or other (e.g., readr) facilities (probably important to read only the relevant columns, for performance) then use GenomicAlignments::cigarWidthAlongReferenceSpace() and similar.

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One more question: what the use of N.regions.removed argument in the function GenomicAlignments::cigarWidthAlongReferenceSpace() ?  

 

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@james-w-macdonald-5106
Last seen 5 hours ago
United States

If  you want to parse a text file, you are probably better off just using perl or awk. You could do this in R, but it's not really designed for fast parsing of text files.

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Frocha ▴ 10
@frocha-12039
Last seen 3.4 years ago

Thanks for both answers!

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