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Issues list

RE: Generating a salmon quantified file for generating cell type specific annotation
#41 by tsetimothy01 was closed Feb 12, 2025
4
Questions about the peak output columns in reproducible_enriched_windows directory
#40 by zhenyu7500 was closed Nov 28, 2024
2
Handling Consecutive Enriched Windows as Merged Peaks
#39 by VandaLovejoy was closed Dec 6, 2024
1
Why are flank and shift used in this analysis pipeline?
#38 by VandaLovejoy was closed Nov 22, 2024
2
RBP bound sequence in repetitive elements (rRNA)
#37 by ychy1 was closed Nov 18, 2024
2
RE: Issue with running skipper in mamba/conda environment
#36 by TimothyTse001 was closed Feb 12, 2025
2
significant difference in read depth between the IP and input data， but some peaks missed
#34 by zhenyu7500 was closed Nov 7, 2024
4
How do I modify skipper_config.py to re-run snakmake with the bam generated earlier in your script
#33 by zhenyu7500 was closed Oct 20, 2024
1
information about intergenic enriched windows
#31 by VandaLovejoy was closed Sep 25, 2024
2
Some misleading in Skipper_config.py
#27 by Lindky was closed Mar 14, 2024
2
Error in rule get_nt_coverage:
#25 by byee4 was closed Mar 2, 2024
4
question about enriched terms
#24 by yos-hida was closed Feb 5, 2024
2
Question about Tested windows.
#20 by FionaMoon was closed Jan 2, 2024
4
How to filter the output of skipper?
#18 by FionaMoon was closed Jul 26, 2024
7
analysis with only 1 SMI sample available
#17 by MSajek was closed Nov 16, 2023
2
[minor] Inconsistent output format between enriched_windows and enriched_re
#16 by algaebrown was closed Oct 12, 2023
1
Paired-end sequencing in Skipper Manifest
#15 by yvazirabad was closed Oct 12, 2023
4
NameError in line 134 of Skipper.py: name 'directory' is not defined File "Skipper.py", line 134, in <module>
#14 by MSajek was closed Feb 12, 2025
6
Execution halted in fit_clip_betabinom.R
#13 by byee4 was closed Jul 11, 2023
3
How to understand parameter INFORMATIVE_READ?
#11 by FionaMoon was closed Jul 7, 2023
5
Execution haulted due to error in rule fit_input_betabinomial_re_model
#9 by ajritter8 was closed Jul 18, 2023
11
Errors when empty reproducible windows file is used as input to consult_term_reference.R
#8 by byee4 was closed Jul 26, 2024
1
finemapped_windows from the manuscript
#7 by CharlotteAnne was closed Jun 7, 2023
3
R scripts appear incompatible with some R packages
#6 by byee4 was closed Apr 28, 2023
2
STAR alignment fails for larger (~80M) datasets due to limitOutSJcollapsed
#4 by byee4 was closed Dec 23, 2022
1
ProTip! What’s not been updated in a month: updated:<2025-02-14.