Hi, I am wondering if it is possible to calculate the percentage each of the four nucleic acids holds in a certain spot in sam file. Here is what I mean using the statement of input and output.
Input : SAM file
Output: Spot 1 : A: 10% , G: 20%, C: 30%, T: 40%
My understanding for these question is to loop through the sam file and for each aligned read, find the nucleotide the questioned spot.
I am wondering if there is a better solution.
2 answers
If you have (or are willing to convert to) BAM files (I think it cannot work with SAM files) we usually use bam-readcount for this kind of data extraction. The output is a bit more complex (and informative) than what you are asking, but it's possible to parse it wit R or similar to get the table you need.
seqtk comp can give you base composition. From there you could easily get percentages with something like awk.
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Instead of %, you can obtain read coverage for each position for each base, with igvtools from bam files. ncxhit
Thanks! I'll check that out
Fyi cpad0112, you can paste plain biostars links, both from posts or users without any
@and the title/username will be displayed automatically ;-)