lweasel/piquant

Issues

• Add threshold for short transcripts

  #62 opened 7 years ago by lweasel
  0

• Mention samtools version tested with in documentation

  #61 opened 8 years ago by lweasel
  0

• Prequantification fails if GTF attribute values contain spaces

  #60 opened 8 years ago by lweasel
  0

• Update ReadTheDocs URLs (.org -> .io)

  #59 opened 9 years ago by lweasel
  0

• Consider the effect of effective length correction (pun intended)

  #58 opened 9 years ago by rob-p
  1

• Bias motif PWM file not copied to correct location during package installation

  #56 opened 9 years ago by lweasel
  1

• Allow relative paths for GTF files

  #57 opened 9 years ago by lweasel
  0

• Clarify "Typical pipeline usage" documentation

  #55 opened 9 years ago by lweasel
  0

• Incorrect demand that "--noise_transcript_gtf" option be specified

  #54 opened 9 years ago by lweasel
  0

• Improve naming of parameters.py etc.

  #15 opened 10 years ago by lweasel
  1

• Add piquant.py option to control no. of threads used by quantifiers etc.

  #18 opened 10 years ago by lweasel
  1

• Implement gene-level accuracy analysis

  #34 opened 10 years ago by lweasel
  1

• Make creation of output directories consistent

  #42 opened 10 years ago by lweasel
  1

• Incorporate "read noise" as a quantification parameter

  #44 opened 10 years ago by lweasel
  2

• Check v1.1 changes under Python 3.4.

  #47 opened 10 years ago by lweasel
  1

• Should be able to specify separate read and quantification parent directories

  #35 opened 10 years ago by lweasel
  1

• Update to latest version of quantification tools

  #41 opened 10 years ago by lweasel
  1

• Incorporate strandedness of reads as quantification parameter

  #43 opened 10 years ago by lweasel
  1

• Prevent negative values of read length, depth etc.

  #45 opened 10 years ago by lweasel
  1

• Add script/command description to usage messages

  #48 opened 10 years ago by lweasel
  1

• Feature Request: Record & report usage statistics for (pre-)quantification steps

  #50 opened 10 years ago by rob-p
  6

• Randomise strand for "unstranded" paired-end reads

  #51 opened 10 years ago by lweasel
  1

• Add units to plot axis labels

  #52 opened 10 years ago by lweasel
  1

• Make NOT_PRESENT_CUTOFF a user-definable option

  #26 opened 10 years ago by lweasel
  1

• Make ERROR_PERCENTAGE_THRESHOLD a user-definable option

  #27 opened 10 years ago by lweasel
  1

• Misspelled parameters in params file are ignored

  #46 opened 10 years ago by lweasel
  0

• Move code from top-level scripts into modules so that it can be tested.

  #11 opened 10 years ago by lweasel
  1

• Tidy writing of commands in prepare_read_simulation

  #36 opened 10 years ago by lweasel
  0

• Consistent structure for scripts

  #10 opened 10 years ago by lweasel
  0

• Tidy calculate_unique_transcript_sequence into functions to allow for testing

  #13 opened 10 years ago by lweasel
  0

• Finish first draft of documentation

  #39 opened 10 years ago by lweasel
  1

• check_reads should check that the right number of reads were created.

  #37 opened 10 years ago by lweasel
  0

• Doc string typo prevents simulate_read_bias script operating

  #40 opened 10 years ago by lweasel
  0

• Move top-level scripts into scripts/ directory

  #23 opened 10 years ago by lweasel
  2

• Make GROUPED_STATS_NUM_TPMS_FILTER user-definable via option

  #29 opened 10 years ago by lweasel
  0

• Define order for fixed parameter values in plot file names/titles

  #28 opened 10 years ago by lweasel
  0

• Deal with ordutils dependency

  #22 opened 10 years ago by lweasel
  1

• Produce consistent set of plots for a single quantification run

  #33 opened 10 years ago by lweasel
  0

• Queries on contents of distribution stats files

  #25 opened 10 years ago by lweasel
  0

• Fix error message for unknown quantification method

  #30 opened 10 years ago by lweasel
  0

• Add option for graph output format

  #32 opened 10 years ago by lweasel
  1

• Race condition in prequantify step.

  #31 opened 10 years ago by lweasel
  0

• Check piquant scripts work with Python 3

  #24 opened 10 years ago by lweasel
  0

• Cleanup of non-essential files not working for RSEM

  #21 opened 10 years ago by lweasel
  0

• Remove --output-genome-bam option when running RSEM

  #19 opened 10 years ago by lweasel
  0

• Temporary read files should be deleted unless -nocleanup is set

  #17 opened 10 years ago by lweasel
  1

• Remove strand-specific quantification options in single-end case

  #20 opened 10 years ago by lweasel
  0

• Strandedness wrong for Cufflinks quantification

  #16 opened 10 years ago by lweasel
  0

• Add transcript GTF file and genome fasta directory into params file

  #14 opened 10 years ago by lweasel
  0

• Full path to bias file needs to be written in run_quantification.sh

  #12 opened 10 years ago by lweasel
  0