calculation of coverage for a given region
I have a region and I want to calculate a coverage per base for each position of this region.
I tried samtools depth and samtools mpileup. They do not show depth == 0. I need it. bedtools coverageBed. Too slow even for one region. Check here. Rsamtools is also too slow to compute everything.
Are there any another tools that will be fast and will output depth ==0?
1 answer
Log in to answer this question.
More posts like this
-
Formula for extracting per base read depth/per base genome coverage from a SAM file?
written by Diploid Progenitor •
-
How to calculate average depth for each Amplicon in targeted amplicon sequencing?
written by bioinfo89 •
-
Where, When and How to use the "breadth of coverage" values reported per bin in BEDtools coverageBE…
written by Zee_S
-
Median coverage from BAM file
written by firestar
-
Depth of Coverage - Calculated Per Probe / Bed Region
written by jnowacki
-
coverageBed misses some reads with the overlap of one basepair
written by tonja.r
-
bedtools coverageBed vs samtools mpileup, speed
written by tonja.r
-
samtools mpileup for multiple regions output in different files
written by tonja.r
-
coverage per base using samtools depth and mpileup
written by tonja.r
-
Normalized coverage histograms for selected chromosome region
written by biotech
With samtools depth it is really easy to infer zero coverage regions.