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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fix umi-tools dependency on python hash function values

#470 TyberiusPrime closed 1 month ago
7
Tests don't pass in released 1.1.1

#469 TyberiusPrime closed 8 months ago
3
Impossible to launch UMI_tools

#468 baliaga31 closed 3 years ago
2
Error running whitelist

#467 prmunn closed 1 year ago
2
group --per-gene for 1.6 million nanopore reads of a PCR amplicon consumes too much memory

#466 gordonrix closed 8 months ago
5
Problems with dedup output and RSEM

#465 lcabus-flomics closed 8 months ago
72
Fixing --whitelist command-line option

#464 jonn-smith closed 2 years ago
1
umi_tools dedup Error: How to solve this problem？

#463 geng-lee closed 3 years ago
2
questions on --output-stats=deduplicate

#462 gemmapuixeu closed 8 months ago
3
AssertionError: not all umis are the same length(!): 4 - 5

#461 MonalisaHota closed 3 years ago
7
Error when using --extract-method=regex

#460 retrogenomics closed 3 years ago
4
Logging broken (python version issue?)

#459 IanSudbery closed 8 months ago
2
dedup removed all reads on a gene

#458 pinbo closed 8 months ago
13
sc rna seq data

#457 yudizhangzyd closed 1 year ago
3
extract error

#456 gitamahm closed 3 years ago
2
Errors picked up by python 3.8's syntax checker

#455 IanSudbery closed 3 years ago
0
[BUG] umi_tools dedup duplicates mates for secondary alignments

#454 RoelKluin closed 8 months ago
17
`filter-out` option no work for SE reads

#453 y9c closed 3 years ago
4
fix read1 error in writing filtered result

#452 y9c closed 3 years ago
3
UMIClusterer speed on large dataset and potential parallelization

#451 coffeebond closed 1 year ago
2
nosetests showing 1 error in python3 (and multiple for python 2.7 with appropriate umi tools version)

#450 alexander-e-f-smith closed 8 months ago
11
The 1.0.1 version doesn't run properly

#449 Kikou33 closed 3 years ago
1
about whitelist of umi_tools

#448 10KGenomics closed 1 year ago
2
Raise warning instead of Errors if no UMI are requested in whitelist

#447 dawe closed 1 year ago
0
added dual barcode correction

#446 Acribbs closed 4 years ago
0
How to extract fastq files with the cell barcode still remained?

#445 vagabond12 closed 8 months ago
5
umi_tools dedup fails with old pysam

#444 sunnymouse25 closed 1 year ago
10
Fix bug with unmapped paired end reads

#443 Daniel-Liu-c0deb0t closed 4 years ago
3
Include cell tag and UMI tag to bam file coming from Cel-Seq2

#442 sarajimenez closed 8 months ago
2
Adding UMI to a tag on both reads in a bam file

#441 SPPearce closed 4 years ago
6
Representative sequences after deduplication not consistent between different runs

#440 zxl124 closed 8 months ago
6
Compromise for errors between cell and discard

#439 mbahin closed 4 years ago
3
umi-tools extract with FASTA files

#438 gallardo-seq closed 8 months ago
4
--filter-out and --filter-out2

#437 nktkee closed 4 years ago
6
umi_tools does not work on unaligned BAM files

#436 dkoppstein closed 1 year ago
4
too little reads left after umi_tools dedup!

#435 windtalker6 closed 4 years ago
25
Enables reads to be processed before end of contig

#434 TomSmithCGAT closed 4 years ago
0
{ts} documentation update

#433 TomSmithCGAT closed 4 years ago
2
images

#432 TomSmithCGAT closed 4 years ago
3
Read pairs do not match???

#431 windtalker6 closed 4 years ago
5
/libk5crypto.so.3: symbol krb5int_utf8s_to_ucs2les, version krb5support_0_MIT not defined in file libkrb5support.so.0 with link time reference

#430 windtalker6 closed 4 years ago
2
after installing with pip3 I get following error: "pkg_resources.DistributionNotFound: The 'python-dateutil>=2.7.3' distribution was not found and is required by pandas"

#429 bkaczkowski closed 4 years ago
2
sam_methods.get_bundle code

#428 miktrinh closed 4 years ago
10
Options to reverse-complement read 2 UMI

#427 eugenechow closed 8 months ago
3
Resolves travis fails

#426 TomSmithCGAT closed 4 years ago
0
How to deal with different UMI length?

#425 tzhu-bio closed 4 years ago
5
Silent out of bounds failure

#424 pati-ni closed 7 months ago
4
Documenting algorithms

#423 TomSmithCGAT opened 4 years ago
0
errors in making whitelist

#422 ayusyarif closed 4 years ago
16
{ts} ignore read pair suffixes

#421 TomSmithCGAT closed 4 years ago
0

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