Hi Gaurav,

good point. Here is what we do
bedToGenePred $pathToTOGAresults/final.bed stdout | genePredToGtf file stdin stdout | gt gtf_to_gff3 -tidy | gt gff3 -tidy -sort -setsource $ref | evmFormatIsoSeq.pl > Evidences/$db.evm.toga.$ref.gff3

I have uploaded the perl script to TOGA/supply/evmFormatIsoSeq.pl
genePredToGtf and bedToGenePred are part of the UCSC kent src code.
Best
Michael

Thanks so much, Michael; super appreciate it.

Best,
Gaurav

Hi,
I am trying to run bedToGenePred $pathToTOGAresults/final.bed stdout | genePredToGtf file stdin stdout | gt gtf_to_gff3 -tidy | gt gff3 -tidy -sort -setsource $ref | evmFormatIsoSeq.pl > Evidences/$db.evm.toga.$ref.gff3

However, the command gt is not recognized and it is not clear to me what $ref means. Could you please clarify these points?

gt --help
Usage: gt [option ...] [tool | script] [argument ...]
The GenomeTools genome analysis system.

-i enter interactive mode after executing 'tool' or 'script'
-q suppress warnings
-test perform unit tests and exit
-seed set seed for random number generator manually.
0 generates a seed from current time and process id
-help display help and exit
-version display version information and exit

Tools:

bed_to_gff3

@DiegoSafian if I could add to what Michael commented:
$ref is the reference genome you used to run TOGA. But in this case, it can be any label that would help EvidenceModeler to distinguish between sources of evidence. You could just use 'toga' label instead.

Hi Gaurav,

good point. Here is what we do bedToGenePred $pathToTOGAresults/final.bed stdout | genePredToGtf file stdin stdout | gt gtf_to_gff3 -tidy | gt gff3 -tidy -sort -setsource $ref | evmFormatIsoSeq.pl > Evidences/$db.evm.toga.$ref.gff3

I have uploaded the perl script to TOGA/supply/evmFormatIsoSeq.pl genePredToGtf and bedToGenePred are part of the UCSC kent src code. Best Michael

Hi, thank you for providing this command. However, when I ran it, the output file showed:
复制
skipping line 1 in file "stdin": unknown feature: "transcript"
skipping line 14 in file "stdin": unknown feature: "transcript"
skipping line 31 in file "stdin": unknown feature: "transcript"
I want to know what causes this and how to fix it. Thanks for your help!

Not sure, but I guess the gff3 format is not what the script expects.
I don't have much experience with gff3, which is a bad, less standardized format.
My suggestion is to take a single gff3 gene and debug this.