gcount: gcount: Obtain Raw Read Counts from RNASeq Data

In openanalytics/gcount: Obtain Raw Read Counts from RNASeq Data

Description

gcount is an R-package that allows to obtain raw read counts quickly and easily from RNASeq data to be used in downstream analyses.

Details

The current functionality is as follows:

• Provide a bam/bed file or object along with gtf/gff file or object as input.

• Specify sequencing type: paired or single end data.

• Specify library type: unstranded, first-strand or second-strand specific.

• 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 – genes, exons, introns etc.

See Also

get_counts

openanalytics/gcount documentation built on May 24, 2019, 2:26 p.m.