aryeelab guideseq issues

aryeelab / guideseq

Analysis pipeline for the GUIDE-seq assay.

GNU Affero General Public License v3.0

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issues

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400mb of .Sam but no off target

#76 piailmitico opened 3 days ago
0
ImportError: cannot import name 'demultiplex' from 'umi'

#75 qicheng-ma opened 3 days ago
0
How to combine multiple samples into one MERGED group in test_manifest.yaml

#74 qicheng-ma opened 4 weeks ago
0
unsupported operand type(s) for +=: 'int' and 'NoneType' in 2024

#73 Ohmori-Insilico opened 3 months ago
0
How to repeat your Results?

#72 Bathroomboss opened 1 year ago
0
Merge dev updates into main

#71 martinaryee closed 1 year ago
0
Merge Tsai lab py2 to py3 changes

#70 martinaryee closed 1 year ago
0
TypeError: load() missing 1 required positional argument: 'Loader'

#69 mhtran145 opened 1 year ago
2
Is sgRNA sequence required to be an input?

#68 Huanle closed 1 year ago
0
First line of data is skipped in `visualize` step

#67 zheins opened 2 years ago
0
Using Pos and Neg strand libraries to identify cleavage events

#66 phoman14 opened 2 years ago
0
yaml with multiple controls

#65 jsacco1 opened 2 years ago
2
Bump pyyaml from 3.11 to 5.4

#64 dependabot[bot] closed 1 year ago
1
Filter step: Background file

#63 jsacco1 opened 3 years ago
1
Update README.md

#62 martinaryee closed 3 years ago
0
python3 ?

#61 colindaven closed 3 years ago
1
Missing index files

#60 nechamaklt11 opened 4 years ago
1
UIMtagg

#59 EMMA-MGH opened 4 years ago
0
Bump pyyaml from 3.11 to 5.1

#58 dependabot[bot] closed 3 years ago
1
Updated link to download guideseq_test_fastq.zip

#57 sowmyaiyer closed 1 year ago
0
Stable branch to use? Or only releases?

#56 cjfields opened 4 years ago
0
unsupported operand type(s)

#55 frankMusacchia opened 5 years ago
9
HTseq

#54 ghost closed 5 years ago
0
Links in large_test.sh are "dead"

#53 JoeEmendo closed 4 years ago
7
Fixed bug where reverse complement off-targets are missed in lower case reference. Fixes #51

#52 martinaryee closed 5 years ago
0
Serious bug in identifyOfftargetSites.py causes bona fide off-targets to be missed

#51 staciawyman closed 5 years ago
6
Test error Offtarget sites are not the same

#50 Zethson closed 5 years ago
2
demultiplex failure

#49 Salvobioinfo opened 5 years ago
4
Fastq downloaded from SRA showing error at identify off-targets step

#48 asgarhussain opened 5 years ago
4
Error while running test data

#47 asgarhussain opened 5 years ago
1
Update identifyOfftargetSites.py

#46 neolei closed 1 year ago
0
build fails. Change test_guideseq.py to output diff between expected output and actual

#45 sowmyaiyer closed 6 years ago
1
Change step1/step2 into more descriptive names

#44 sowmyaiyer closed 6 years ago
0
absorb split_pipeline branch into dev/master

#43 sowmyaiyer opened 6 years ago
0
Draft release notes for v1.1

#42 martinaryee opened 6 years ago
1
Add blacklist sites and filtering instructions to README

#41 martinaryee opened 6 years ago
0
Add SNP calling code and usage instructions

#40 martinaryee opened 6 years ago
0
failure to demultiplex manifest

#39 wconnell opened 6 years ago
4
Add an output table that is filtered for sites present in control and sites without a sequence match

#38 martinaryee opened 7 years ago
0
Parameter --window_size for Cas9 in command line

#37 josemalo opened 7 years ago
0
Too many files open during demultiplex

#36 michael-weinstein opened 7 years ago
4
Umi module

#35 michael-weinstein closed 7 years ago
3
Threading option for bwa mem step

#34 biobenkj opened 7 years ago
9
Error in pip install -r requirements.txt

#33 robyn-ball closed 7 years ago
2
Log run information and dependency versions to output folder

#32 josemalo opened 7 years ago
0
Fixed visualization to ensure adequate image height

#31 vedtopkar closed 7 years ago
0
Candidate v1.0.1 release

#30 martinaryee closed 8 years ago
0
How to deal with single-end FASTQ sequences form Hiseq2500 with guideseq?

#29 xueweireally opened 8 years ago
0
How to generate index FASTQ files?

#28 xueweireally opened 8 years ago
4
Updated for compliance with pep8

#27 vedtopkar closed 8 years ago
1