From 165c5a0c8db580be8de33328550ef94b93f9008d Mon Sep 17 00:00:00 2001 From: Adam Cribbs Date: Sun, 15 Oct 2023 11:55:13 +0100 Subject: [PATCH] Update pipeline_count.py --- tallytrin/pipeline_count.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tallytrin/pipeline_count.py b/tallytrin/pipeline_count.py index e28fc42..9f5772a 100644 --- a/tallytrin/pipeline_count.py +++ b/tallytrin/pipeline_count.py @@ -228,7 +228,7 @@ def mapping_trans(infile, outfile): writes the output to the specified outfile. ''' - statement = '''minimap2 -ax splice:hq -uf %(cdna_fasta)s %(infile)s > %(outfile)s 2> %(outfile)s.log''' + statement = '''minimap2 map-ont -p 0.9 --end-bonus 10 -N 3 %(cdna_fasta)s %(infile)s > %(outfile)s 2> %(outfile)s.log''' P.run(statement, job_options='-t 24:00:00')