Shore srna
From SHORE wiki
The purpose of shore srna is facilitating the analysis of small RNA sequencing data. The genome is scanned for regions where significant amounts of small RNAs are expressed and annotates these loci by read counts as well as the sRNA size that predominates.
Usage: shore srna [OPTIONS] [SAMPLE_PATHS]
| Mandatory | ||
| -s, --samples=<arg[:...][,...]> | Shore directories (comma-separated; colon-separated items will be treated as a single assay) | |
| -o, --outfolder=<arg> | (Default: SrnaAnalysis) | Output directory |
| Segmentation | ||
| -j, --joint-seg | Apply segmentation threshold to the joint coverage instead of per-sample coverage | |
| -C, --static-threshold=<arg> | (Default: 10) | Coverage threshold [>] |
| -J, --minsize=<arg> | (Default: 15) | Segment size threshold [>=] |
| -V, --probation=<arg> | (Default: 0) | Allow a mitigated threshold for at most <arg> base pairs inside a segment |
| -Q, --mitigator=<arg> | (Default: 1) | Modifier for calculation of the mitigated threshold, value in [0,1] |
| -v, --overlap=<arg> | (Default: 1) | Required overlap for merging segments (may be negative to allow gaps) |
| Alignment filter | ||
| -H, --hits-range=<arg,arg> | Set the allowed range of repetitiveness ('1,1' = nonrep reads) | |
| -M, --mm-range=<arg,arg> | Set the allowed range of mismatches | |
| -R, --region=<arg> | Only use reads that overlap with the range [chr1:pos1..[chr2:]pos2] | |
| --assume-length=<arg> | (Default: 400) | Assume maximal alignment length <arg>, enables fast range queries |
| -B, --duplicates=<arg> | Report at maximum <arg> reads with the 5' end at the same position on the same strand | |
| --sam-ref=<arg> | Reference sequence for SAM file parsing | |
| --peflags=<arg[,...]> | Use only reads with the given PE flag(s) | |
