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How to generate cDNA file from genome FASTA and GTF?

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 The organism that I work with, Ciona intestinalis is not a model organism, so the files on Ensembl are outdated.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?

cdna scrna-seq
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updated by iraun iraun • written by ipeknaz • ipeknaz

1 answer

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)

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written by dsull dsull

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