v.3.3.0#43
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Implement the ability to use the "both" option for "tx_discovery", which will run Bambu and Stringtie2 and merge their gtfs together. The rest of the pipeline is performed on the merged file.
- Modified workflow to ensure that all novel transcripts (both known and novel genes) will go through FEELnc - Started implementing isoform visualisation
Fix issue when only input file is used with StringTie
- Fixed problem where MSTRG genes assigned to reference genes where still present in final count matrix. These are now removed by using gtf produced by FORMAT_GFFCOMPARE instead of the raw gtf produced by STRINGTIE:MERGE. - Publish count matrix in final output when using "both" option
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--tx_discovery both).--feelnc_mRNA,--feelnc_lncRNA) (default 3,000; minimim 100).