From c3c5f7ba653c716b6e012f9aabfaf50ca97bc5ea Mon Sep 17 00:00:00 2001 From: Jon Palmer Date: Mon, 17 Feb 2020 10:52:25 -0800 Subject: [PATCH] add --aligners to help menu in train/update --- scripts/funannotate | 2 ++ 1 file changed, 2 insertions(+) diff --git a/scripts/funannotate b/scripts/funannotate index 105ef259..8dc47ac9 100644 --- a/scripts/funannotate +++ b/scripts/funannotate @@ -132,6 +132,7 @@ Optional: -m, --min_coverage Min depth for normalizing reads. Default: 5 --pasa_db Database to use. Default: sqlite [mysql,sqlite] --pasa_alignment_overlap PASA --stringent_alignment_overlap. Default: 30.0 + --aligners Aligners to use with PASA: Default: minimap2 blat [gmap] --max_intronlen Maximum intron length. Default: 3000 --species Species name, use quotes for binomial, e.g. "Aspergillus fumigatus" --strain Strain name @@ -245,6 +246,7 @@ Optional: --pasa_config PASA assembly config file, i.e. from previous PASA run --pasa_db Database to use. Default: sqlite [mysql,sqlite] --pasa_alignment_overlap PASA --stringent_alignment_overlap. Default: 30.0 + --aligners Aligners to use with PASA: Default: minimap2 blat [gmap] --max_intronlen Maximum intron length. Default: 3000 --min_protlen Minimum protein length. Default: 50 --alt_transcripts Expression threshold (percent) to keep alt transcripts. Default: 0.1 [0-1]