Longest Isoform using CAFE
Hi AT, Don’t know if you get this. I am having trouble finding longest isoform using CAFÉ. Here is the code:
export PATH=/programs/CAFE-4.2.1:$PATH cafe python python_scripts/cafetutorial_longest_iso.py -d /home/mk2565/wordir/mk2565/LeaF_protein/ cat /home/mk2565/wordir/mk2565/LeaF_protein/longest*.fa > /home/mk2565/wordir/mk2565/makeblastdb_input.fa
LeaF_protein is the directory with fasta seq exactly mentioned n the CAFÉ tutorial. After running this code I get makedbfile.fasta but its empty and the code runs for days 4-5 with nothing.
Thanks Mayank
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cafe python python_scripts ...does not seem logically correct way of running this. I formatted your command using thecodeoption but perhaps it did not correctly format. If those are multiple commands e.g.catis on a separate line then please edit/reformat original post.Some other options: How to extract the longest isoform from multi fasta file if you are only looking for the longest transcript.
Hi Genomax,
thanks for response. Here it is: CAFE
I took a brief look at the CAFE manual but don't see this program listed. I am not near a computer to check on this but this looks like it is an accessory script in CAFE program.
cafe python blahstill appears to be incorrect way of running it. If this is from tutorial then it definitely should not take 4-5 days to run.All CAFE commands.txt
Tutorial files I am referring this!