Using GTF2 to generate a filtered FASTA and transcript-gene map

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#1

Hi,

I am very new to galaxy and with no knowledge in Bioinformatics. I’m trying to analyze some scRNA seq data from Cryptococcus neoformans.
I’ve been trying (unsuccessfully) to use the GTF2GeneList tool to generate the filtered FASTA and transcript gene-map using a GTF file and FASTA file downloaded from the NCBI (https://www.ncbi.nlm.nih.gov/assembly/GCF_000149245.1/), for later running Alevin

Every time I run the tool the same error appears: Fatal error: Exit code 1 ().
I’d appreciate if you could tell me what’s that meaning and if you have any suggestions.

Thanks a lot for the help.

Best wishes,
Diana T.

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#2

Welcome, @Diana_Patricia_Tamay !

Maybe it won’t work because you’re using NCBI version:

What it does

Given an Ensembl GTF file, it will extract all information on chromosomes, coordinates, and attributes provided at the specified feature level. Mitochondrial features can also be flagged.

You can download from Ensembl Fungi here

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#3

Dear David,

Thanks soooooo much!!! I struggled a lot and the solution was so easy and obvious (for you ;)).
Infinite thanks!

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#4

You’re welcome, @Diana_Patricia_Tamay.
If you don’t mind, I’d like to advise you to be sure about selecting the right strain, since there are ~41 assemblies of C. neoformans and I tend to see people that don’t care about it, which can be a bias sometimes.

#5

Thanks so much! That is a very good point. I did check this :wink:

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