aryeelab/guideseq

Issues

• argparse bug when running consolidate

  #78 opened 3 months ago by racng
  0

• AttributeError: 'GuideSeq' object has no attribute 'primer1'

  #77 opened 5 months ago by qicheng-ma
  0

• 400mb of .Sam but no off target

  #76 opened 6 months ago by piailmitico
  0

• ImportError: cannot import name 'demultiplex' from 'umi'

  #75 opened 6 months ago by qicheng-ma
  0

• How to combine multiple samples into one MERGED group in test_manifest.yaml

  #74 opened 7 months ago by qicheng-ma
  0

• unsupported operand type(s) for +=: 'int' and 'NoneType' in 2024

  #73 opened 9 months ago by Ohmori-Insilico
  0

• How to repeat your Results?

  #72 opened a year ago by Bathroomboss
  0

• Fastq downloaded from SRA showing error at identify off-targets step

  #48 opened 6 years ago by asgarhussain
  4

• TypeError: load() missing 1 required positional argument: 'Loader'

  #69 opened 2 years ago by mhtran145
  2

• How to generate index FASTQ files?

  #28 opened 9 years ago by xueweireally
  4

• unsupported operand type(s)

  #55 opened 5 years ago by frankMusacchia
  9

• Is sgRNA sequence required to be an input?

  #68 opened 2 years ago by Huanle
  0

• First line of data is skipped in `visualize` step

  #67 opened 3 years ago by zheins
  0

• Using Pos and Neg strand libraries to identify cleavage events

  #66 opened 3 years ago by phoman14
  0

• yaml with multiple controls

  #65 opened 3 years ago by jsacco1
  2

• Filter step: Background file

  #63 opened 4 years ago by jsacco1
  1

• Missing index files

  #60 opened 5 years ago by nechamaklt11
  1

• python3 ?

  #61 opened 4 years ago by colindaven
  1

• UIMtagg

  #59 opened 5 years ago by EMMA-MGH
  0

• Links in large_test.sh are "dead"

  #53 opened 5 years ago by JoeEmendo
  7

• Stable branch to use? Or only releases?

  #56 opened 5 years ago by cjfields
  0

• HTseq

  #54 opened 6 years ago
  0

• Make real test dataset available

  #11 opened 9 years ago by martinaryee
  7

• Serious bug in identifyOfftargetSites.py causes bona fide off-targets to be missed

  #51 opened 6 years ago by staciawyman
  6

• failure to demultiplex manifest

  #39 opened 7 years ago by wconnell
  4

• demultiplex failure

  #49 opened 6 years ago by Salvobioinfo
  4

• Too many files open during demultiplex

  #36 opened 8 years ago by michael-weinstein
  4

• Test error Offtarget sites are not the same

  #50 opened 6 years ago by Zethson
  2

• Error while running test data

  #47 opened 6 years ago by asgarhussain
  1

• Change step1/step2 into more descriptive names

  #44 opened 7 years ago by sowmyaiyer
  0

• build fails. Change test_guideseq.py to output diff between expected output and actual

  #45 opened 7 years ago by sowmyaiyer
  1

• absorb split_pipeline branch into dev/master

  #43 opened 7 years ago by sowmyaiyer
  0

• Draft release notes for v1.1

  #42 opened 7 years ago by martinaryee
  1

• Add blacklist sites and filtering instructions to README

  #41 opened 7 years ago by martinaryee
  0

• Add SNP calling code and usage instructions

  #40 opened 7 years ago by martinaryee
  0

• Add an output table that is filtered for sites present in control and sites without a sequence match

  #38 opened 8 years ago by martinaryee
  0

• Parameter --window_size for Cas9 in command line

  #37 opened 8 years ago by josemalo
  0

• Threading option for bwa mem step

  #34 opened 8 years ago by biobenkj
  9

• Umi module

  #35 opened 8 years ago by michael-weinstein
  3

• Error in pip install -r requirements.txt

  #33 opened 8 years ago by robyn-ball
  2

• Log run information and dependency versions to output folder

  #32 opened 8 years ago by josemalo
  0

• How to deal with single-end FASTQ sequences form Hiseq2500 with guideseq?

  #29 opened 9 years ago by xueweireally
  0

• Add ReverseComplementIndexRead2 option

  #21 opened 9 years ago by shengdar
  2

• Full PEP8 Compliance

  #14 opened 9 years ago by vedtopkar
  1

• Test dataset for guideseq package

  #16 opened 9 years ago by shengdar
  3

• Automatically strip whitespace from YAML input

  #17 opened 9 years ago by vedtopkar
  1

• filterBackgroundSites.py doesn't respect the bedtools path from the YAML

  #19 opened 9 years ago by martinaryee
  1

• Add ability to specify multiple backgrounds to filter out

  #13 opened 9 years ago by vedtopkar
  0

• Add optional parameters to manifest for greater flexibility

  #15 opened 9 years ago by vedtopkar
  0

• Additional code commenting for clarity

  #12 opened 9 years ago by martinaryee
  0