processGsnapResults: Process Gsnap RNA-Seq BAM output
Description
Resumes RNA-seq pipeline after aligning with gsnap consolidating
outputUsage
processGsnapResults(options, merged_gsnap_output,
preprocess_fastq_list, call_variants=TRUE)Arguments
options
An HTSeqGenieBase::pipelineOptions object
merged_gsnap_output
the BAM output from gsnap
preprocess_fastq_list
a list of results obtained from
processing the raw fastqs prior to alignment
Details
given a BAM-file output from gsnap (with the MD tag), resumes the
RNA-seq pipeline, which includes counting hits to exons, genes,
transcripts, etc. and quantifying miRNA/ncRNA contaminatino