Tools to assess coverage and error rate at specific position
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Entering edit mode
3.8 years ago
prishly ▴ 10

Hi, Sorry for the question that's probably been asked by many. I need to know coverage and error rate of my reads at any specific position of the reference. Can any alignment tool like LAST or BWA do that and all I need after alignment is a sam/bam file viewer that'll give me metrics for any position I choose? And I don't need assembly for that, right?

P.S. I did take some effort and took a quick look at what's available but I haven't found a list of specific metrics that any given tool outputs. Plus I have very little time to tell if the quality of sequencing fits our goals.

alignment sequencing error rate coverage • 899 views
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Entering edit mode
3.8 years ago

Have a look at pysamstats. You could execute it like this:

pysamstats \
--fasta ref.fa \
--type variation \
aln.bam


to get a table of matches and mismatches at each position.

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Entering edit mode
3.8 years ago
Wietje ▴ 220

FeatureCounts could do the job I assume. You'd need to align your data first, for instance with HISAT2, which gives you a sam-format as output that you could enter into FeatureCounts (a tool in Subread --> http://subread.sourceforge.net/) . You additionally need an annotation file (e.g. in GTF format) and FeatureCount then counts the reads at feature or meta-feature level (exons or genes for example). Would that help you?