Error while running gffread.

[ambarishK]

I am getting an error while running gffread.

No fasta index found for genomeref.fa. Rebuilding, please wait..
Error: sequence lines in a FASTA record must have the same length!

[ambarishK]

I normalized fasta file which solve above error.

Now I am getting 0 byte output while running gffread on merged gtf.

0 bytes
format fasta  database?
No fasta index found for genomeref.fa. Rebuilding, please wait..
Fasta index rebuilt.

[bgruening]

@ambarishK this is not an error. Can you share your history?

[ambarishK]

Sir, this is the accessible link to my history - https://usegalaxy.eu/u/ambarishk/h/de-novo

[bgruening]

@ambarishK take off the "fasta file with spliced CDS for each GFF transcript (-x cds.fa)" "protein fasta file with the translation of CDS for each record (-y pep.fa)" ... you don't have CDS records.

Then it will work.

[ambarishK]

Thank you so much sir. It worked.

Now I am moving for abundance estimation of gene expression.

I am trying to quantify them using align and estimate abundance method - a trinity tool. It askes for transcript to gene map file. I am generating gene to transcript map file using RSEM gene to transcript map tool. But quantification fails.