CGATOxford UMI-tools issues

CGATOxford / UMI-tools

Tools for handling Unique Molecular Identifiers in NGS data sets

MIT License

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issues

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Documentation for prepare-for-rsem.

#670 IanSudbery opened 2 days ago
0
Option --no-sort-output with dedup

#669 Rayan21100 opened 3 days ago
4
ModuleNotFoundError: No module named 'umi_tools' with Python 3.9

#668 MelinaKlostermann closed 2 days ago
5
dedup STAR transcriptome file using umi_tools

#667 aayushraman closed 1 week ago
1
--per-cell behavior with multiple read_id barcodes

#666 peterpdu closed 4 weeks ago
1
Add workflow to push releases to pypi

#665 eachanjohnson opened 1 month ago
2
v1.1.5 kicking out one of pair of discordant reads ; v1.1.1 not showing same behaviour

#664 alexander-e-f-smith opened 1 month ago
12
No v1.1.6 on conda, and only prebuilt for MacOS (no source) on pypi

#663 eachanjohnson opened 1 month ago
3
python3.12 support as release

#662 alexander-e-f-smith closed 1 month ago
2
UMItools extract with nanopore long reads

#661 ctarpey opened 2 months ago
2
Issue with group and dedup option

#660 LioLenr opened 3 months ago
0
AssertionError: not all umis are the same length(!): 48 - 49

#659 ChrisSteel-bio closed 2 months ago
2
Update Python versions for tests

#658 sebastian-luna-valero closed 1 month ago
3
Rebuilt _dedup_umi.c using cython 3.0.11

#657 IanSudbery closed 3 months ago
1
"Installing from source" failed on 'PyLongObject' error

#656 djunsheep closed 3 months ago
1
Update testing suite to pytest

#655 eachanjohnson closed 1 month ago
9
Make count_tab compatible with `umi_tools extract`

#654 eachanjohnson closed 3 months ago
1
UMI tools with paired end

#653 LioLenr closed 3 months ago
1
umi tools 1.1.5 not available on pypi

#652 johandahlberg closed 3 months ago
2
Output of `umi_tools extract` not compatible with `umi_tools count_tab`

#651 eachanjohnson closed 3 months ago
2
UMI-Tools does not remove all duplicate reads

#650 Redmar-van-den-Berg closed 3 months ago
8
Filter for low read-depth UMIs?

#649 gdlampe closed 1 month ago
1
Documentation improvement suggestion

#648 hazmup opened 5 months ago
2
Unmapped and unpaired reads retained even when selected not to.

#647 hazmup closed 5 months ago
9
UMI-tool 1.1.5 not working with --per-gene --per-contig --gene-transcript-map

#646 pclavell opened 5 months ago
6
'extract' is not a UMI-tools command.

#645 yueli8 closed 1 month ago
6
Update setup.py

#644 IanSudbery closed 5 months ago
1
TypeError: 'encoding' is an invalid keyword argument for this function

#643 yueli8 closed 1 month ago
3
provide an explicit list of cell barcodes to whitelist?

#642 bbimber opened 6 months ago
5
[QUESTION] Recommended RNAseq total experiment UMI read coverage

#641 MrKevinDC closed 6 months ago
3
change back to original matplotlib backend

#640 sshen8 closed 6 months ago
3
UMI-tools duplicated removal

#639 mwylerCH closed 7 months ago
2
samtools error in umi-tools dedup

#638 rfreeman7 closed 1 month ago
2
Umitools Deduplication with STAR Alignment

#637 hserio closed 7 months ago
4
UMI_tools whitelist function not taking set-cell-number into account

#636 Victoria-01 closed 8 months ago
6
group method: not all UMI-containing reads assigned UG tag

#635 epiliper opened 8 months ago
7
Are UMI reads not sequenced more than once removed during dedup step?

#634 goyastephanie closed 7 months ago
1
UMI_extract for paired end reads of micro_RNA

#633 oneito closed 7 months ago
2
Add issue templates

#632 TomSmithCGAT closed 5 months ago
7
Add FAQ entry re identification of possible duplicates reads/pairs

#631 TomSmithCGAT closed 8 months ago
2
adds option to extract barcode from read2 only

#630 TomSmithCGAT closed 8 months ago
2
Improve docs re chimeric/unmapped/unpaired read pairs

#629 TomSmithCGAT closed 8 months ago
0
Resolves pandas aggregation warnings

#628 TomSmithCGAT closed 8 months ago
1
Compilation fails on python 3.12

#627 s-andrews closed 1 month ago
8
AssertionError: files /scratch/tmpqkgmy2lv/stdout and tests/whitelist_umi_output.sam are not the same

#626 vasquini closed 9 months ago
4
Dedup error: 'a' cannot be empty unless no samples are taken

#625 NordinZandhuis closed 9 months ago
2
Dedup errors if input BAM file is empty

#624 IanSudbery opened 10 months ago
2
umi_tools extract: UMI on 5' read 1 and 3' read 2

#623 lzt5269 closed 1 month ago
2
Is newer version of UMI-tools compatible with dedup_umi.py in this repo?

#622 kvn95ss closed 10 months ago
2
UMI-tools dedup and heavily soft-clipped CIGAR strings due to overlapping PE reads...

#621 SJJHK closed 1 month ago
1