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add: readme for delstop

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kuoi 2024-12-09 17:37:16 +11:00
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README.md
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@ -135,15 +135,21 @@ grep '>' Reference.fasta | sed "s@>@@g" > genes
### sortdiamond ### sortdiamond
Usage: sortdiamond diamond_output.m8 generated.fasta sseq,qstart,qend,bitscore/evalue,qseq(optional, default 1,6,7,11,17, start from 0) bitscore/evalue(optional, default bitscore) Usage: `sortdiamond diamond_output.m8 generated.fasta sseq,qstart,qend,bitscore/evalue,qseq(optional, default 1,6,7,11,17, start from 0) bitscore/evalue(optional, default bitscore)`
Default sseq is column 2, qstart is column 8, etc. Default sseq is column 2, qstart is column 8, etc.
Diamond default output format (--outfmt 6) does not contain qseq, you must custom the output format under output format 6. Diamond default output format (--outfmt 6) does not contain qseq, you must custom the output format under output format 6.
### delstop
`delstop <fasta_aa> <fasta_nt> --delete`
Delete StopCondon generated by Macse. fasta_aa and fasta_nt should be macse output files, `--delete` should be used when downstream software is tirmal
### splitfasta ### splitfasta
Usage: splitfasta sample.fasta Usage: `splitfasta sample.fasta`
It always creates directories in the path that you run the splitfasta, and puts split fasta into the directory. It always creates directories in the path that you run the splitfasta, and puts split fasta into the directory.