Closed BarryDigby closed 4 years ago
Hi Barry,
You need to look at the next line of the fasta as Novoindex line count is zero based.
Colin
Hi, Barry,
I think you might use the wrong file :sweatsmile:, you should use "gencode.v33lift37.pctranscripts.fa.gz", not "gencode.v33lift37.pc_translations.fa".
tw
@colinhercus Thanks for the information!
@BarryDigby At https://www.gencodegenes.org/human/release_33lift37.html
head -5 gencode.v33lift37.pc_translations.fa.gz
ENSP00000493376.2|ENST00000641515.2_2|ENSG00000186092.6_4|OTTHUMG00000001094.4_4|OTTHUMT00000003223.4_2|OR4F5-202|OR4F5|326| MKKVTAEAISWNESTSETNNSMVTEFIFLGLSDSQELQTFLFMLFFVFYGGIVFGNLLIV ITVVSDSHLHSPMYFLLANLSLIDLSLSSVTAPKMITDFFSQRKVISFKGCLVQIFLLHF FGGSEMVILIAMGFDRYIAICKPLHYTTIMCGNACVGIMAVTWGIGFLHSVSQLAFAVHL
You should be using ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_33/GRCh37_mapping/gencode.v33lift37.pc_transcripts.fa.gz
Thank god for that, much less work for all involved ;)
thanks again gents
Hi there,
create_reference.py
fails with the following error:Inspecting the line in question:
This seems to be a novoalign problem, BWA creates the index without issue.
Please find attached the error log.
nclscan.err.txt