From d3e6ad053b61f421126e17c0f1599bfbd2d28d4f Mon Sep 17 00:00:00 2001 From: luc Date: Fri, 29 Mar 2024 09:36:17 -0400 Subject: [PATCH] fix getting read length issue for single index --- demux_run_dag.py | 1 + scripts/get_sequencing_read_data.py | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/demux_run_dag.py b/demux_run_dag.py index 6c85c45..09f010a 100644 --- a/demux_run_dag.py +++ b/demux_run_dag.py @@ -171,6 +171,7 @@ def stats(ds, **kwargs): # check if the run is 10X by read length atac, use_bases_mask = scripts.get_sequencing_read_data.main(sequencer_path) + print("read length: {}".format(use_bases_mask)) if use_bases_mask == [29, 89] or atac: # if is atac run, demux is using cellranger mkfastq if atac: diff --git a/scripts/get_sequencing_read_data.py b/scripts/get_sequencing_read_data.py index bdcab04..e8e16f7 100755 --- a/scripts/get_sequencing_read_data.py +++ b/scripts/get_sequencing_read_data.py @@ -36,7 +36,7 @@ def get_sequencing_read_data(sequencer_path): use_bases_mask = "Y" + str(reads_tag[0][1]) + ",I" + str(reads_tag[1][1]) + ",Y" + str(reads_tag[2][1]) + ",Y" + str(reads_tag[3][1]) else: atac = False - use_bases_mask = [reads_tag[0][1], reads_tag[3][1]] + use_bases_mask = [reads_tag[0][1], reads_tag[-1][1]] return(atac, use_bases_mask)