LRGASP/lrgasp-submissions

Issues

• show have a pipeline name as well as submitter name

  #48 opened 2 years ago by diekhans
  0

• reference_transcript_id attribute not validated

  #47 opened 3 years ago by diekhans
  0

• additional challenge 2 submission

  #46 opened 3 years ago by mei-du
  2

• Comma-separated column names do not match libraries in experiment.json

  #44 opened 3 years ago by andrewprzh
  2

• Challenge 3, long_short, Illumina + ONT dRNA submission

  #45 opened 3 years ago by andrewprzh
  1

• lrgasp-synapse-download doesn't handle specifying a single file

  #43 opened 3 years ago by diekhans
  0

• mismatch between data matrix and synapse for simulated data id

  #42 opened 3 years ago by diekhans
  0

• Unspecified parameter in model description

  #41 opened 3 years ago by andrewprzh
  0

• simulation software mixup

  #38 opened 3 years ago by julienlag
  1

• python virtual environment for submission/validation tools

  #34 opened 3 years ago by julienlag
  1

• conflicting info on simulated data sample identifiers

  #39 opened 3 years ago by julienlag
  1

• lrgasp-tools ambiguous output

  #35 opened 3 years ago by julienlag
  1

• lrgasp-validate-entry looks for non-gz files

  #36 opened 3 years ago by julienlag
  1

• creating a team in Synapse is mandatory

  #37 opened 3 years ago by julienlag
  1

• unused reads in read-to-model map file format

  #33 opened 3 years ago by julienlag
  1

• Define process for transfering files, recommend tools.

  #6 opened 3 years ago by diekhans
  5

• document required login for synypse

  #29 opened 3 years ago by diekhans
  1

• add new Sequel II subread BAMs to the RNA-Seq data matrix

  #30 opened 3 years ago by julienlag
  2

• PB adapters

  #28 opened 3 years ago by Lutri22
  2

• provide flowcell and kit version for ONT datasets

  #8 opened 4 years ago by julienlag
  1

• add aligner and parameters to metadata

  #24 opened 4 years ago by diekhans
  1

• `challenge_id` and `submission_type` metadata attributes should be better described

  #19 opened 4 years ago by julienlag
  1

• File format conversion scripts for output from specific tools

  #15 opened 4 years ago by fairliereese
  1

• ID column must be called “ID”, not IDs, nor transcript_id ...

  #20 opened 4 years ago by diekhans
  2

• Do we need a separate JSON for the read to model map?

  #14 opened 4 years ago by cindyeliang
  2

• read id to model format

  #11 opened 4 years ago by fairliereese
  4

• consistency of transcript_id's in model GTF vs expression matrix

  #16 opened 4 years ago by julienlag
  1

• Extra tab in one submitter

  #21 opened 4 years ago by diekhans
  2

• submission with IDs that do not match GTF

  #22 opened 4 years ago by diekhans
  2

• duplicate ids in different genes

  #23 opened 4 years ago by diekhans
  2

• valid Python-style identifier

  #18 opened 4 years ago by julienlag
  1

• Gene vs. transcript level expression

  #17 opened 4 years ago by fairliereese
  2

• The Illumina GM12878 pilot data ENCSR000AEH does not include SIRVs

  #12 opened 4 years ago by julienlag
  3

• The submission.json example is 404

  #9 opened 4 years ago by julienlag
  1

• The challenge_id json property is misspelled

  #10 opened 4 years ago by julienlag
  1