# rnaseq_Sf
Recipe source code: https://github.com/rworkflow/RcwlRecipes/blob/master/Rcwl/pl_rnaseq_Sf.R (opens new window)
# plot
# Inputs
| label | type | description | |
|---|---|---|---|
| in_seqfiles | File[] | ||
| in_prefix | string | ||
| in_genomeDir | Directory | ||
| in_GTFfile | File | ||
| in_runThreadN | int |
# Outputs
| label | type | description | |
|---|---|---|---|
| out_fastqc | File[] | ||
| out_BAM | File | ||
| out_Log | File | ||
| out_Count | File | ||
| out_stat | File | ||
| out_count | File | ||
| out_distribution | File | ||
| out_gCovP | File | ||
| out_gCovT | File |
# steps
| label | doc | |
|---|---|---|
| fastqc | ||
| STAR | ||
| sortBam | ||
| samtools_index | ||
| samtools_flagstat | ||
| featureCounts | ||
| gtfToGenePred | ||
| genePredToBed | ||
| r_distribution | ||
| gCoverage |
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