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Question about UMI deduplication step when starting from BAM files

Status: Open.

#29 In salzman-lab/SICILIAN;

· CCCBBG opened on Jun 11, 2025

class_input_secondary is commented out

Status: Open.

#28 In salzman-lab/SICILIAN;

· QuanlongJiang opened on Oct 12, 2024

Enhancement step: updating <code>light_utils.py</code> to run with current Pandas &amp; Numpy when there are no junctions

Status: Open.

#26 In salzman-lab/SICILIAN;

· fomightez opened on Jul 25, 2024

[404] Page not found: https://github.com/salzman-lab/nf-sicilian?tab=readme-ov-file

Status: Open.

#25 In salzman-lab/SICILIAN;

· Whistick opened on Jun 21, 2024

Error processing Gencode GTF

Status: Open.

#23 In salzman-lab/SICILIAN;

· mblanche opened on Apr 22, 2024

domains file :i could not find domains file

Status: Open.

#22 In salzman-lab/SICILIAN;

· lancy-liang opened on May 1, 2023

create annotator from 10x references genes.gtf.gz

Status: Open.

#21 In salzman-lab/SICILIAN;

· leezx opened on Mar 13, 2023

EXITING: because of fatal INPUT file error: could not open read file

Status: Open.

#20 In salzman-lab/SICILIAN;

· TinyTasy opened on Nov 15, 2022

AssertionError: bam_read1.query_name==bam_read2.query_name

Status: Open.

#18 In salzman-lab/SICILIAN;

· zyh4482 opened on Oct 15, 2022

The detection of 10X single-cell transcriptome gene fusion

Status: Open.

#17 In salzman-lab/SICILIAN;

· chuiqin opened on Sep 24, 2022

Index Error when trying to run create_annotator.py

Status: Open.

#10 In salzman-lab/SICILIAN;

· gabee-chan opened on Mar 28, 2022