From b3429e9d74df5cf1477aea129458bc5637fb639b Mon Sep 17 00:00:00 2001 From: Guoyi Zhang Date: Mon, 9 Dec 2024 17:37:16 +1100 Subject: [PATCH] add: readme for delstop --- README.md | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 66457b1..54d05f6 100644 --- a/README.md +++ b/README.md @@ -135,15 +135,21 @@ grep '>' Reference.fasta | sed "s@>@@g" > genes ### 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. Diamond default output format (--outfmt 6) does not contain qseq, you must custom the output format under output format 6. +### delstop + +`delstop --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 -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.