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CGATOxford
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UMI-tools
Tools for handling Unique Molecular Identifiers in NGS data sets
MIT License
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Handle `--per-contig` grouping with no gene tags
#570
mfansler
closed
1 year ago
2
question about how to prepare bam
#569
anoronh4
closed
1 year ago
1
group with `--per-contig` unnecessarily requires gene tags
#568
mfansler
closed
1 year ago
5
Inconsistent result of no reads from the same coordinate in UMI-tools dedup
#567
camelest
closed
1 year ago
1
ops
#566
mariafrancesca21
closed
2 years ago
0
Does concatenating fastq files cause any issues
#565
Joseph-Waldron
closed
2 years ago
2
UMI reads are more than Fastq reads
#564
zhangpicb
closed
2 years ago
4
Python 3.11 support?
#563
sjaenick
closed
1 year ago
11
Dedup outputting empty BAM
#562
richardsalisbury
closed
1 year ago
1
Limit memory usage of dedup ("Killed")
#561
cf-nb
closed
1 year ago
1
AssertionError: not all umis are the same length - Why is this an assertion?
#560
exsquire
closed
2 years ago
2
KeyError: "tag 'NH' not present"
#559
shah0829
closed
1 year ago
2
Fixing syntax warning in extract.py
#558
rajivnarayan
closed
2 years ago
1
--ignore-tlen slow running
#557
alexander-e-f-smith
closed
1 year ago
3
--multimapping-detection-method Options documentation
#556
gavin-peng
closed
1 year ago
1
bam dedup (umi_tools dedup)
#555
HengkuanLi
closed
8 months ago
10
About customized tag in sam file
#554
baozijoe
closed
2 years ago
2
skip adding comment lines
#553
hukai916
closed
2 years ago
2
umi_tools extract error
#552
fpengstudy
closed
2 years ago
5
Add option to specify UMI separator in extract - Merge of PR #548 and…
#551
janoppelt
closed
2 years ago
1
makes umi_tools deterministic with --random-seed
#550
TomSmithCGAT
closed
1 month ago
8
Add option to specify UMI separator in extract 2
#549
janoppelt
closed
2 years ago
6
Add option to specify UMI separator in extract
#548
janoppelt
closed
2 years ago
1
How to generate a spreedsheet showing total reads, mapped reads, total UMIs ,gene numbers etc per cell?
#547
Meletian
closed
8 months ago
1
Ts add test action
#546
TomSmithCGAT
closed
2 years ago
2
all zero expression genes
#545
wangjiawen2013
closed
2 years ago
1
UMI dedup
#544
lkerr34
closed
2 years ago
2
Speed up writing mates
#543
IanSudbery
closed
2 years ago
1
Fix test_umi_tools.py
#542
IanSudbery
closed
2 years ago
0
Filtering cell barcodes not in the whitelist
#541
chrarnold
closed
2 years ago
6
Unexpected difference between dedup with and without per-cell
#540
chrarnold
closed
2 years ago
2
Problems with UMI dedup and time when aligned against transcriptome
#539
lcabus-flomics
closed
2 years ago
21
when add the parameter --ignore-umi ， why the count matrix only 1 and 0?
#538
omicsclass
closed
2 years ago
2
Altered if clasuses around selection of commands in umi_tools.py
#537
IanSudbery
closed
2 years ago
8
Conda issue: IndexError: list index out of range
#536
CWYuan08
closed
2 years ago
3
umi_tools count Pysam Error
#535
ethanqiu04
closed
1 year ago
1
Only softclip of 2bp at start of read distinguishes it from another read with same barcode
#534
alexander-e-f-smith
closed
8 months ago
4
umitools dedup error: '<' not supported between instances of 'str' and 'bytes'
#533
camelest
closed
2 years ago
5
Is a whitelist necessary for 'umi_tools extract --extract-method=regex'
#532
wanxinw
closed
8 months ago
2
umitools extract command ignores provided whitelist file
#531
Aintzane99
closed
2 years ago
4
Problem of quantification with htseq
#530
lkw159159
closed
1 year ago
3
Error-correcting cell barcodes
#529
TomSmithCGAT
closed
1 year ago
1
Cannot solve the '--no-pg' issue
#528
lkw159159
closed
2 years ago
5
umi-tools extract
#527
wangjiawen2013
closed
2 years ago
4
Could I keep the I1&R1&R2.fastq.gz as their original format after the extraction?
#526
yuw444
closed
2 years ago
4
Custom whitelist
#525
MEFarhadieh
closed
2 years ago
11
Counting issue: failed to map segment from shared object
#524
CWYuan08
closed
1 year ago
3
Analysis problem sorted out
#523
parichitran
closed
2 years ago
0
bc-pattern2: TypeError: object of type 'NoneType' has no len()
#522
m3hdad
closed
8 months ago
6
Changing the word "stdin" to "stdout" in the doc
#521
k3yavi
closed
2 years ago
2
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