[EMBOSS] getorf output discrepancy

Narayana.Upadhyaya at csiro.au Narayana.Upadhyaya at csiro.au
Wed Jul 27 09:30:09 UTC 2011

I figured out the problem. Missing ORFs in NT output are the ones which are just 198 NT length. When I put minsize 198 for NT output I don't miss anything.

Sorry for bothering.



I am trying to get both NT and AA sequence out puts from a file with ~20,000 transcripts  models using the getorf with following command:-

getorf -minsize 200 -reverse Y  myfile.fa -find 3
getorf -minsize 200 -reverse Y myfile.fa -find 1

I get the outputs all right. But I was expecting same number of sequences in both (with identical names in the header). But looks like at 60 odd sequences(which are there in the AA output) are missing in the NT out put.

Can anyone explain this discrepancy?  I tried putting the minsize option as "201" for both but the problem persists.



More information about the EMBOSS mailing list