How to generate cDNA file from genome FASTA and GTF?

Question

[ipeknaz]

Hello! I am new to single-cell RNASeq and am currently trying to run Kallisto | bustools to make a pseudoalignment. The organism that I work with, Ciona intestinalis is not a model organism, so the files on Ensembl are outdated. I have its genome in FASTA format and a GTF file from collaborators, but I need the cDNA file to run my pipeline. Is there any tool to build a cDNA file from the genome and GTF?

[iraun]

Maybe of interest: Extract sequences from a FASTA file using a gtf file

Answer 1

[dsull]

Yes, you can use kb-python to generate such files.

pip install kb_python
kb ref -i index.idx -g t2g.txt -f1 cdna.fa reference.fasta annotation.gtf 

The only files you need to provide above are reference.fasta and annotation.gtf

The kallisto index, index.idx, will be generated, as will the cDNA fasta (cdna.fa) and a file showing which transcripts correspond to which genes (t2g.txt)