Rsamtool or Rbamtools function to view the number of reads between a range
what is Equivalent R function for the command line below?
samtools view yourBAMfile.bam chr1:567876-568100 | wc -l
How should I approach.
I got a GRanges object with seqnames, start and end. I would like to count the number of reads between each range in the GRange object in a BAM file in R
• 2,101 views
•
link
updated
by
Devon Ryan
•
written
by
startup_biostar •
•
written
by
startup_biostar •
1 answer
rbamtools directly provides a count function (bamCount), so just go with that.
• 1 views
•
link
written
by
Devon Ryan
Log in to answer this question.
More posts like this
-
Adding gene to GRange objects with single base
written by QX •
-
Granges manipulation
written by Bastien Hervé
-
why makeGRangesFromDataFrame don't do the IRange
written by michelafrancesconi8 •
-
Keep metadata gc column using GenomicRanges
written by Begonia_pavonina •
-
GRanges: remove ranges that falls in between a larger range?
written by simplitia •
-
GRanges: merge metadata from the same ranges
written by arseru •
-
How to obtain distinct/uniqe rows from GenomicRanges object
written by gundalav
-
Avoid intersection of adjacent regions in GenomicRanges::intersect()
written by david.mas •
-
[SOLVED] Trying to apply overlap to each row of a "GRangesList"
written by User 7754
-
Accessing start positions in a strand-specific manner from a GRanges object
written by R. Taylor Raborn
