Difference between revisions of "Shore mapdisp"
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(Created page with ''''shore mapdisp''' provides text-based alignment visualization in the terminal. There are lots of much more sophisticated programs for viewing short read alignments. This tool i…') |
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specific region of the genome. | specific region of the genome. | ||
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'''Usage:''' shore mapdisp [OPTIONS] SHORE_PATHS | '''Usage:''' shore mapdisp [OPTIONS] SHORE_PATHS | ||
Latest revision as of 10:01, 28 September 2011
shore mapdisp provides text-based alignment visualization in the terminal. There are lots of much more sophisticated programs for viewing short read alignments. This tool is rather designed for extremely rapid inspection of the alignments in a specific region of the genome.
Command line options
Usage: shore mapdisp [OPTIONS] SHORE_PATHS
| Output | ||
| --outfile=<arg> | Write to output file instead of using less | |
| Display | ||
| -d, --no-color | Do not use color terminal | |
| Read filtering | ||
| -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) | |
