# rnaseq_quant
Recipe source code: https://github.com/rworkflow/RcwlRecipes/blob/master/Rcwl/pl_rnaseq_quant.R (opens new window)
# plot
# Inputs
| label | type | description | |
|---|---|---|---|
| in_fq1 | File | ||
| in_fq2 | File | ||
| in_prefix | string | ||
| in_genomeDir | Directory | ||
| in_GTFfile | File | ||
| in_runThreadN | int | ||
| salmon_index | Directory |
# Outputs
| label | type | description | |
|---|---|---|---|
| out_BAM | File | ||
| out_Log | File | ||
| out_junction | File | ||
| out_stat | File | ||
| out_count | File | ||
| out_salmon | Directory | ||
| out_rdist | File |
# steps
| label | doc | |
|---|---|---|
| STAR | ||
| sortBam | ||
| samtools_index | ||
| samtools_flagstat | ||
| featureCounts | ||
| gtfToGenePred | ||
| genePredToBed | ||
| r_distribution | ||
| salmon |
← rnaseq Sf strelka2PL →