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biocoder / Perl-for-Bioinformatics

An attempt to help anyone interested in using Perl for Bioinformatics
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Option for totally de novo ncRNA analysis #7

Closed alexweisberg closed 8 years ago

alexweisberg commented 8 years ago

I was wondering how feasible it would be to add an option for an analysis with no reference ncRNAs. That is, when I run my analysis using a reference genome from NCBI genbank, it gives an error message since there are no annotated ncRNAs in the reference. This is further compounded by the fact that NCBI gff files typically do not include "protein_coding" tags in gff files (which can be converted to gtf using gffread).

If I try to specify "CUSTOM" and give it an empty gtf file for known ncRNA's, it also gives an error when it tries to parse the empty file.

Would it be possible to disable the known ncRNA portion of the analysis?

alexweisberg commented 8 years ago

This is definitely a case of my not reading the manual enough before posting. Running the individual portions of the pipeline separately (along with the --skip-get option) allowed me to analyze purely novel ncRNAs.