Collect metrics from a RNAseq BAM file
meta
Groovy Map containing sample information e.g. [ id:‘test’, single_end
bam
BAM/SAM file
*.{bam,sam}
ref_flat
Genome ref_flat file
gene_pred
genome gene_pred file as an alternative to the ref_flat file
fasta
Genome fasta file
rrna_intervals
Interval file of ribosomal RNA regions
metrics
RNA alignment metrics files generated by picard
*.rna_metrics
pdf
Plot normalized position vs. coverage in a pdf file generated by picard
versions
File containing software versions
versions.yml
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
