lweasel / piquant

A pipeline to assess the quantification of transcripts.

http://piquant.readthedocs.org/en/latest/

lweasel/piquant Issues

Add threshold for short transcripts
Updated 7 years ago
Mention samtools version tested with in documentation
Updated 7 years ago
Prequantification fails if GTF attribute values contain spaces
Updated 7 years ago
Update ReadTheDocs URLs (.org -> .io)
Updated 8 years ago
Consider the effect of effective length correction (pun intended)
Updated 8 years ago1
Bias motif PWM file not copied to correct location during package installation
Closed 8 years ago1
Allow relative paths for GTF files
Updated 8 years ago
Clarify "Typical pipeline usage" documentation
Updated 8 years ago
Incorrect demand that "--noise_transcript_gtf" option be specified
Updated 8 years ago
Improve naming of parameters.py etc.
Closed 9 years ago1
Add piquant.py option to control no. of threads used by quantifiers etc.
Closed 9 years ago1
Implement gene-level accuracy analysis
Closed 9 years ago1
Make creation of output directories consistent
Closed 9 years ago1
Incorporate "read noise" as a quantification parameter
Closed 9 years ago2
Check v1.1 changes under Python 3.4.
Closed 9 years ago1
Should be able to specify separate read and quantification parent directories
Closed 9 years ago1
Update to latest version of quantification tools
Closed 9 years ago1
Incorporate strandedness of reads as quantification parameter
Closed 9 years ago1
Prevent negative values of read length, depth etc.
Closed 9 years ago1
Add script/command description to usage messages
Closed 9 years ago1
Feature Request: Record & report usage statistics for (pre-)quantification steps
Closed 9 years ago6
Randomise strand for "unstranded" paired-end reads
Closed 9 years ago1
Add units to plot axis labels
Closed 9 years ago1
Make NOT_PRESENT_CUTOFF a user-definable option
Closed 9 years ago1
Make ERROR_PERCENTAGE_THRESHOLD a user-definable option
Closed 9 years ago1
Misspelled parameters in params file are ignored
Closed 10 years ago
Move code from top-level scripts into modules so that it can be tested.
Closed 10 years ago1
Tidy writing of commands in prepare_read_simulation
Closed 10 years ago
Consistent structure for scripts
Closed 10 years ago
Tidy calculate_unique_transcript_sequence into functions to allow for testing
Closed 10 years ago
Finish first draft of documentation
Closed 10 years ago1
check_reads should check that the right number of reads were created.
Closed 10 years ago
Doc string typo prevents simulate_read_bias script operating
Closed 10 years ago
Move top-level scripts into scripts/ directory
Closed 10 years ago2
Make GROUPED_STATS_NUM_TPMS_FILTER user-definable via option
Closed 10 years ago
Define order for fixed parameter values in plot file names/titles
Closed 10 years ago
Deal with ordutils dependency
Closed 10 years ago1
Produce consistent set of plots for a single quantification run
Closed 10 years ago
Queries on contents of distribution stats files
Closed 10 years ago
Fix error message for unknown quantification method
Closed 10 years ago
Add option for graph output format
Closed 10 years ago1
Race condition in prequantify step.
Closed 10 years ago
Check piquant scripts work with Python 3
Closed 10 years ago
Cleanup of non-essential files not working for RSEM
Closed 10 years ago
Remove --output-genome-bam option when running RSEM
Closed 10 years ago
Temporary read files should be deleted unless -nocleanup is set
Closed 10 years ago1
Remove strand-specific quantification options in single-end case
Closed 10 years ago
Strandedness wrong for Cufflinks quantification
Closed 10 years ago
Add transcript GTF file and genome fasta directory into params file
Closed 10 years ago
Full path to bias file needs to be written in run_quantification.sh
Closed 10 years ago