Closed ckuenne closed 2 years ago
Thanks for catching this, I have updated the instructions in the README to reflect this. I am currently out of the office, If you don't mind, we can leave this Issue up until I come back to the office next week and I can make more thorough testing. In the meantime if someone else has issues than can refer to this post.
hi,
i followed your description for extraction of a refFlat file from ucsc based on encode annotation (https://github.com/mflamand/Bullseye, point 2.). this lead to a crash of Find_edit_site.pl:
this is due to a wrong format of the refflat file, where the first field is missing (gene name):
default gtfToGenePred on encode gtfs will also not work, because it misses the same field.
workaround 1: use ucsc table browser as you described, additionally add field name2, rearrange file to have the correct order of columns (#name2 name chrom strand txStart txEnd cdsStart cdsEnd exonCount exonStarts exonEnds)
workaround 2: use gtfToGenePred on encode gtf with parameter -genePredExt, remove unnecessary columns and move gene_id up front
gtfToGenePred -genePredExt homo_sapiens.104.mainChr.gtf homo_sapiens.104.mainChr.genepredext