Table 1.
icSHAPE pipeline file input and output names.
| Step | Input | Output |
|---|---|---|
| Read collapse | libX.fastq | libX.rmdup.fastq |
| Read trimming | libX.rmdup.fastq | libX.trimmed.fastq |
| Read mapping | libX.trimmed.fastq | libX.sam (*) |
| Transcript abundance estimation | libX.sam | libX.rpkm (*) |
| RT-stop calculation | libX.sam, libX.rpkm | libX.rt (*) |
| Replicate combining | libX.rt, libY.rt, libZ.rt … | background.rt or target.rt |
| RT-stop normalization | background.rt Or Target.rt | background.normalized.rt Or target.normalized.rt |
| Enrichment reactivity score calculation |
background.normalized.rt and target.normalized.rt | icSHAPE.tmp.out (*) |
| Valid score filtering | icSHAPE.tmp.out | icSHAPE.out (*) |
We suggest keeping some important intermediate files (denoted with an asterisk (*)) that will allow rapid rerunning of the icSHAPE pipeline under different parameter settings.