Comments (2)
Hey @amizeranschi , thank you for highlighting that. The problem refers to the gtf provided more than to the --gencode option. The pipeline has been designed to work with all the genomes and annotations, so we are going to fix that issue by changing some default options in the configuration file, leaving those IDs only for testing purpose.
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Could you please share a bit of info about how this issue has been fixed?
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Related Issues (16)
- dexseq: stager.R: subscript out of bounds. HOT 2
- prepare_genome gencode HOT 2
- check_contrastsheet not identifying headers even though they're present HOT 2
- DRIMSEQ_FILTER error HOT 10
- ERROR ~ No such variable: Exception evaluating property 'out' for nextflow.script.ChannelOut HOT 7
- SUPPA cluster events error HOT 14
- GTF_2_GFF3 fails with latest Gencode GTF for human HOT 21
- MISO_SASHIMI step fails when using scratch directory HOT 2
- MISO_SASHIMI looks in NXF_HOME subdirectory instead of working directory for output files HOT 4
- EDGER_EXON fails if only single entry in contrast sheet HOT 1
- STAGER error: subscript out of bounds HOT 6
- The pipeline should be able to infer strandedness from FASTQ (i.e. allow "auto" for strandedness in the CSV) HOT 2
- Error with rmats.py when running with multiple contrasts: <filename>.bam not found in .rmats files HOT 10
- MISO_SASHIMI error: Could not find MISO output files HOT 4
- test profile: miso_index failure HOT 19
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