Shore coverage
From SHORE wiki
For analysis of expression levels of mRNAs and small RNAs or for detection of unknown transcripts it is typically required to generate a coverage graph and to define expressed segments based on consecutive coverage.
shore coverage generates a coverage graph by sequentially scanning the alignment and basically counting reads.
Command line options
Usage: shore coverage [OPTIONS] [MAPFILES]
| Input | ||
| -m, --mapfiles=<arg[:...][,...]> | Alignment files or shore directories (flowcell, lane, pe or barcode; comma-separated; colon-separated items will be treated as single assay) | |
| -n, --merge-input | Merge all input files | |
| Output | ||
| -o, --output-directory=<arg> | (Default: CoverageAnalysis) | Output directory (will be created) |
| -s, --segmentation | Write segmentation files | |
| -t, --merge-segments=<arg> | Overlap in base pairs for merging segment files (may be negative to allow gaps); if unspecified, segments will not be merged | |
| -q, --no-coverage | Do not write coverage files | |
| -z, --compress | Compress output files | |
| --rplot | Plot the specified range using R | |
| --ylim=<arg> | Set y axis limit for plots (default: auto) | |
| --phasing=<arg> | Visualize <arg>-mer phasing | |
| 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 |
| -X, --p3fix=<arg> | Set the 3' end to a fixed distance from the 5' end | |
| -N, --read-lengths=<arg[,...]> | Use only reads of the given length(s) | |
| -T, --strand=<arg> | Use only reads from the given strand | |
| -B, --duplicates=<arg> | Report at maximum <arg> reads with the 5' end at the same position on the same strand | |
| --wpoiss=<arg> | Window size for adaptive duplicate read filtering | |
| --sam-ref=<arg> | Reference sequence for SAM file parsing | |
| --peflags=<arg[,...]> | Use only reads with the given PE flag(s) | |
| Coverage | ||
| -W, --weight-repetitive=<arg> | (Default: divide) | How to weight repetitive hits (divide or multiply or const) |
| Segmentation | ||
| -C, --static-threshold=<arg> | (Default: 10) | Coverage threshold [>] for static segmentation |
| -J, --minsize=<arg> | (Default: 20) | Segment size threshold [>=] for static or dynamic segmentation |
| -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] |
| -D, --dynamic | Switches to dynamic segmentation | |
| -S, --window-size=<arg> | (Default: 2000) | Sliding window size for dynamic segmentation |
| -P, --poisson-threshold=<arg> | (Default: 0.05) | Poisson probability threshold [<=] for dynamic segmentation |
