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Commits on Feb 11, 2019

• output dir simplified

  Accio

  committedFeb 11, 2019
  6cd368d

• sbatch instead of bash

  Accio

  committedFeb 11, 2019
  28b3aa4

• updated content

  Accio

  committedFeb 11, 2019
  215ddcd

• document the correct use of .overlap

  Accio

  committedFeb 11, 2019
  fd420de

Commits on Feb 6, 2019

• use overlap instead of envelop for intervaltree

  Accio

  committedFeb 6, 2019
  9abeb69

Commits on Feb 3, 2019

• use default STAR parameters whenever feasible, ignoreing limits, alignIntro, alignMates, alginSJDB, sjdb

  Accio

  committedFeb 3, 2019
  93dcdc9

Commits on Feb 2, 2019

• add merged

  Accio

  committedFeb 2, 2019
  7407716

• move the description to the top

  Accio

  committedFeb 2, 2019
  2974499

• exported conda env

  Accio

  committedFeb 2, 2019
  e802091

• use more threads and workers to improve the speed

  Accio

  committedFeb 2, 2019
  a8c3254

• don't need to copy the pdf

  Accio

  committedFeb 2, 2019
  a28e4f4

• add my major edits

  Accio

  committedFeb 2, 2019
  5fe4b13

• ignore certain files

  Accio

  committedFeb 2, 2019
  1d988b0

• the intervaltree package in python dropped .search(begin,end, strict=True) from the version 3.0, now uses envelop (which corresponds to strict=True)

  Accio

  committedFeb 2, 2019
  6c20030

• use two workers

  Accio

  committedFeb 2, 2019
  68a9840

• use 1 thread

  Accio

  committedFeb 2, 2019
  eab2a57

• since loading genomeinto shared memory turned out to be problematic on our HPCmachine, I commented out the part of STAR loading genome. Instead, each process loads its own genome copy

  Accio

  committedFeb 2, 2019
  0c9e1b9

• (1) cells indices used are explicitly specified as C[num]+, which are encoded in the 'Corresponding Cell ID code' column in the annotation file (2) no shared memory is used since currently this bre…

  Accio

  committedFeb 2, 2019
  4ee1be0

Commits on Feb 1, 2019

• correct name

  Accio

  committedFeb 1, 2019
  e5fd5ae

• the correct code

  Accio

  committedFeb 1, 2019
  cb6b34b

• use the correct cell index file

  Accio

  committedFeb 1, 2019
  fb0f81f

• luigid had problem with background

  Accio

  committedFeb 1, 2019
  30438ab

• slurm running

  Accio

  committedFeb 1, 2019
  8852d92

• pipeline

  Accio

  committedFeb 1, 2019
  a24c9db

• use my own samples

  Accio

  committedFeb 1, 2019
  76a3ba1

• fix identation problems

  Accio

  committedFeb 1, 2019
  9bcb408

Commits on Dec 20, 2018

• Cap excel sheetname to max 31 chars

  rpadmanabhan

  committedDec 20, 2018
  14ad3b5

Commits on Dec 13, 2018

• Updated criteria for running secondary analysis

  rpadmanabhan

  committedDec 13, 2018
  6908394

Commits on Nov 14, 2018

• Trap UserWarning from demultiplex_cells module

  rpadmanabhan

  committedNov 14, 2018
  132aca5

• Add cutoff for number of cells to run secondary analysis

  rpadmanabhan

  committedNov 14, 2018
  1da0802

Commits on Nov 8, 2018

• Refactor demux (#16)

  rpadmanabhan

  committedNov 8, 2018
  6e7e276

Commits on Nov 5, 2018

• Fix function call

  rpadmanabhan

  committedNov 5, 2018
  79ac354

• Parameterize Genome Build and Annotation information for Run Summary Excel file

  rpadmanabhan

  committedNov 5, 2018
  fc87472

• add drosophila

  rpadmanabhan

  committedNov 5, 2018
  62c49f2

Commits on Nov 2, 2018

• Allow Ns in regex

  rpadmanabhan

  committedNov 2, 2018
  aaab448

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