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Ribo-Seq Samtools pileup

I have the results of samtools mpileup.

ref|NC_001133|  32065   A       17      .....^".^".^".^".^!.^".^".^".^".^".^".^".       
ref|NC_001133|  32066   G       18      ..................      C@1C.1CCCCCCCCCCCC
ref|NC_001133|  32067   A       22      ......................  CC98?C91?CCC;;CCCC;C;C
ref|NC_001133|  32068   T       21      .....................   CCCCCCCCCCCCCCCCCCCCC

What I want to do is use the gene start and stop position in the reference GFF file to create a table of counts across each gene in the genome.

for example:

 gene-1 position1   position2   position3 .....

           17             18           19

Is there a simple way to convert the mpileup results into a table like this? Thank you,

samtools pileup
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written by mplace • mplace

Hi Mike! It's jess ;)

I'm not clear on what you are trying to generate. Do you want the per-base coverage value for each gene in the GFF from start codon to stop codon such that the table will have a different number of columns for each gene?

Would bedtools coverage get you close to what you are looking for? https://bedtools.readthedocs.io/en/latest/content/tools/coverage.html

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written by jv jv

I have mapped Ribo-Seq data and need to see the base coverage across each gene in the GFF. I will check out bedtools.
Thank you.

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written by mplace • mplace

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