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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UMI-Tools does not remove all duplicate reads

#650 Redmar-van-den-Berg opened 5 days ago
3
Filter for low read-depth UMIs?

#649 gdlampe opened 3 weeks ago
0
Documentation improvement suggestion

#648 hazmup opened 1 month ago
2
Unmapped and unpaired reads retained even when selected not to.

#647 hazmup closed 3 weeks ago
9
UMI-tool 1.1.5 not working with --per-gene --per-contig --gene-transcript-map

#646 pclavell opened 1 month ago
4
'extract' is not a UMI-tools command.

#645 yueli8 opened 1 month ago
3
Update setup.py

#644 IanSudbery closed 3 weeks ago
1
TypeError: 'encoding' is an invalid keyword argument for this function

#643 yueli8 opened 1 month ago
2
provide an explicit list of cell barcodes to whitelist?

#642 bbimber opened 1 month ago
5
[QUESTION] Recommended RNAseq total experiment UMI read coverage

#641 MrKevinDC closed 1 month ago
3
change back to original matplotlib backend

#640 sshen8 closed 2 months ago
3
UMI-tools duplicated removal

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

#638 rfreeman7 opened 2 months ago
2
Umitools Deduplication with STAR Alignment

#637 hserio closed 2 months ago
4
UMI_tools whitelist function not taking set-cell-number into account

#636 Victoria-01 closed 3 months ago
6
group method: not all UMI-containing reads assigned UG tag

#635 epiliper opened 3 months ago
7
Are UMI reads not sequenced more than once removed during dedup step?

#634 goyastephanie closed 3 months ago
1
UMI_extract for paired end reads of micro_RNA

#633 oneito closed 3 months ago
2
Add issue templates

#632 TomSmithCGAT closed 2 weeks ago
7
Add FAQ entry re identification of possible duplicates reads/pairs

#631 TomSmithCGAT closed 3 months ago
2
adds option to extract barcode from read2 only

#630 TomSmithCGAT closed 3 months ago
2
Improve docs re chimeric/unmapped/unpaired read pairs

#629 TomSmithCGAT closed 3 months ago
0
Resolves pandas aggregation warnings

#628 TomSmithCGAT closed 3 months ago
1
Compilation fails on python 3.12

#627 s-andrews opened 4 months ago
3
AssertionError: files /scratch/tmpqkgmy2lv/stdout and tests/whitelist_umi_output.sam are not the same

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

#625 NordinZandhuis closed 4 months ago
2
Dedup errors if input BAM file is empty

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

#623 lzt5269 opened 5 months ago
2
Is newer version of UMI-tools compatible with dedup_umi.py in this repo?

#622 kvn95ss closed 5 months ago
2
UMI-tools dedup and heavily soft-clipped CIGAR strings due to overlapping PE reads...

#621 SJJHK opened 5 months ago
1
umi_tools extract --> error saying 'extract' is not a UMI-tools command

#620 mdu4003 closed 4 months ago
3
Collapse barcode to generate whitelist based on frequency

#619 ashokpatowary closed 6 months ago
0
umi extract

#618 robinycfang closed 4 months ago
2
UMIs lost after STAR alignment

#617 asadatae closed 4 months ago
4
Best way to handle non-UMI labelled reads

#616 kvn95ss closed 4 months ago
5
Potential problem with Pandas

#615 kvn95ss closed 3 months ago
1
umi_tools dedup with gene-tag on, how are those reads with "GN:Z:-" tag deduplicated?

#614 MengjunWu closed 7 months ago
2
geneset.gtf location

#613 wwinnerhoo closed 4 months ago
4
umi_tools not "extracting" any barcodes, while the same command had worked before

#612 kvn95ss closed 2 months ago
4
{is} fix read suffix line end

#611 IanSudbery closed 7 months ago
0
Issue with extraction method, obtaining empty file as an output

#610 PavithraV0223 closed 4 months ago
6
{is} prepare for rsem

#609 IanSudbery closed 7 months ago
8
Estimate sequencing error rate

#608 phillipeloher closed 8 months ago
2
prepare-for-rsem no longer works

#607 anoronh4 closed 4 months ago
2
How can use umi-tools for umi present on read1 and in both the end like 5' and 3' end?

#606 unique379r closed 4 months ago
4
Custom UMI Deduplication

#605 jamesboot closed 8 months ago
2
doc: fix docs for dedup stats filenames

#604 msto closed 8 months ago
1
Confused with the output "position" of group function

#603 yinzhuo0322 closed 4 months ago
4
paired-end reads where UMI is located in read 2

#602 silvia1234567890 closed 3 months ago
5
Wrong UMI extracted using Regex

#601 NordinZandhuis closed 11 months ago
0