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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UMItools dedup: It seems that when using '--unmapped/unpaired-reads=use' the unmapped read of a pair is discarded and the mapped counterpart is retained. This leads to genuine singletons/orphan reads (no paired read at all in dedup output ) when in fact it would have had a partner in input file which had an unaligned status. Id this the intended behaviour of the tool?

#520 alexander-e-f-smith closed 8 months ago
3
use of '--unmapped/unpaired-reads=use' read pairs; unmapped read of pair dicarded, mapped kept.

#519 alexander-e-f-smith closed 2 years ago
3
before deduplication BAM file size:102M and after deduplication it is severly reduced to 378K

#518 parichitran closed 8 months ago
12
group stats differ by large amount with use of --ignore-tlen in --paired mode

#517 ijhoskins closed 2 years ago
4
Handling and outputting unmapped reads in dedup module

#516 alexander-e-f-smith closed 1 year ago
6
Error: UMI lengths are not the same!

#515 iammrtza closed 2 years ago
1
umi_tools dedup ValueError: max() arg is an empty sequence

#514 prmunn closed 2 years ago
1
What does the "Found xxxxxxx total reads matching the selected cell barcodes" in whitelist logfile mean

#513 RuiyuRayWang closed 2 years ago
2
umi_tools dedup error

#512 diwasri closed 8 months ago
2
Minimum python version (>=3.5) needs bumping up

#511 gmnelson closed 8 months ago
3
Insert missing "options" in test for white list conditions

#510 IanSudbery closed 2 years ago
0
filtered-out option error

#509 camelest closed 2 years ago
10
cell bases required in pattern for whitelist; unclear documentation

#508 cmatKhan closed 2 years ago
2
AssertionError: not all umis are the same length(!): 6 - 7

#507 Matt-Schmitz closed 2 years ago
6
Fix "umi_tools command" prints stack trace

#506 epruesse closed 2 years ago
1
Settings for the analysis of bulk-RNAseq with 11 bp UMI

#505 kate-simonova closed 8 months ago
3
comparison with alevin.

#504 mortunco closed 2 years ago
2
Segmentation fault

#503 ljharrison1 closed 2 years ago
5
Error: parsing fastq file

#502 CWYuan08 closed 2 years ago
15
How to collapse reads in bam from the result of UMI-tools group

#501 camelest closed 2 years ago
2
umi_tools extract error when providing with a white list

#500 robinycfang closed 8 months ago
7
PyPi doesn't have 1.1.2 release

#499 wjdingman1 closed 2 years ago
4
Justify the choice of 3 in whitelist_methods::getKneeDistance()

#498 hukai916 closed 2 years ago
1
Will --ignore-read-pair-suffixes turn on or turn off the "ignore"?

#497 realzhang closed 2 years ago
4
Whitelist: Can't proceed beyond "finding putative error cell barcodes"

#496 kasayadior closed 2 years ago
4
total_counts_post = total_counts_pre ?!

#495 YichaoOU closed 2 years ago
1
Error when running umi_tools whitelist TypeError: can only concatenate str (not "NoneType") to str

#494 singlecellfan closed 8 months ago
9
one read to multiple unique_id?

#493 YichaoOU closed 1 year ago
6
How is mapping coordinates for UMI group defined?

#492 YichaoOU closed 3 years ago
2
whitelist error :Syntax error near unexpected symbol ` ('

#491 jehuliu closed 2 years ago
3
Converting UMI-Tools output into correct format for cHiC analysis

#490 aturocks closed 1 year ago
1
about UMI error correction

#489 10KGenomics closed 2 years ago
2
Getting UMI-tools to work with pyston (python replacement)

#488 jelber2 closed 3 years ago
2
Get number of reads per UMI, irrespective of mapping position

#487 nickforino closed 2 years ago
3
On Mac 11.4, four different errors following homebrew procedure

#486 bgphd closed 1 year ago
2
umit-tools count ends with TypeError: '<' not supported between instances of 'int' and 'str'

#485 yuifu closed 3 years ago
2
misleading default in help text

#484 bernt-matthias closed 3 years ago
1
Error with sam input for dedup

#483 bernt-matthias closed 1 year ago
1
Obtaining error for parsing fastq file

#482 kpatankar closed 1 year ago
2
.bai not found

#481 bgphd closed 3 years ago
4
Extracting UMI into read header and removing trailing sequence

#480 abracarambar closed 3 years ago
3
Using group/dedup --random-seed and PYTHONHASHSEED=0

#479 alexander-e-f-smith closed 3 years ago
1
fgbio and umi-tools, and called variant with vardict, umi-tools get 8 times variants than fgbio

#478 worker000000 closed 3 years ago
15
umi in 5 end of both R1 and R2

#477 worker000000 closed 1 year ago
21
count_tab, view UMI clusters

#476 phillipeloher closed 1 year ago
0
Deduplicating bam files without UMIs

#475 SPPearce closed 3 years ago
6
Memory issue

#474 sameerh closed 1 year ago
3
optional UMI

#473 idot closed 3 years ago
2
Release notes not up to date

#472 IanSudbery closed 3 years ago
2
--filtered-out doesn't work

#471 Freequilibrium closed 3 years ago
5

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