gcount is an R-package that allows to obtain raw read counts
quickly and easily from RNASeq data to be used in downstream analyses.
The current functionality is as follows:
bam/bed file or object along with gtf/gff
file or object as input.
Specify sequencing type:
single end data.
Specify library type:
Filter reads based on number of mismatches prior to counting if necessary.
Consider or ignore reads that map to overlapping genes.
Count reads that overlap feature of interest –
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