Change Log
JCAST software for alternative splicing proteomics analysis. Create custom protein databases using RNA-seq data to identify unique protein alternative splicing isoforms in mass spectrometry experiments
Abstract
This page provides the documentation for the JCAST package, which is a tool for create a database of protein isoforms from RNA-seq data.
v0.3.5a
- JCAST will now skip a junction if the nucleotide sequence contains masked bases
- Added the –mask argument to determine masked nucleotide letters (default: NnXx)
- Added an option to translate only a subset of splice types (MXE, RI, SE, A3SS, A5SS) with the -s argument
v0.3.5
- Fixed an issue where a small number of slices were not translated.
- Fixed an issue where JCAST quits if the model flag is not set.
v0.3.2
- The -q –qvalue option now works by including splice junctions within the specified range. To preserve the previous behavior, use -q 0.01 1. The default -q 0 1 disables filtering.
- The -c –canonical argument now defaults to False. To preserve prior behaviors, manually set the -c flag to translate canonical proteins detected in the RNA-seq experiments even if isoform translation failes
- The -c –canonical argument now will translate a canonical sequence even if a splice event has low skipped junction counts or falls outside of the specified fdr range
- JCAST now automatically models the likely translatable junction count threshold through the -m –model argument. Previously this was done manually then set as an integer (minimal read count) using the -r –read argument.
- The skipped junction counts used for modeling now consider the sum of all biological and technical replicates rather than the minimum
v0.3.1
- Fixed issues where Gencode GTF files without transcript_biotype annotations could not be read
- Fixed issues of retrieving Uniprot canonical sequences from Ensembl transcript versions
- Compatibility with biopython>=1.78
v0.2.8
- Fixed an issue where jcast is called twice from the direct cli entry point
- Added option to use longest coding sequence from GTF as canonical
v0.2.6
- Fixed an issue where some A5SS minus-strand transcripts had incorrect phases retrieved from gtf
- Fixed an issue where some transcripts using a secondary translation start sites are not trimmed