How to generate cDNA file from genome FASTA and GTF?
1
0
Entering edit mode
12 months ago
ipeknaz • 0

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 The organism that I work with, Ciona intestinalis is not a model organism, so the files on Ensembl are outdated.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 • 771 views
ADD COMMENT
0
Entering edit mode
ADD REPLY
0
Entering edit mode
12 months ago
dsull ★ 6.2k

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)

ADD COMMENT

Login before adding your answer.

Traffic: 2246 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6