Understanding how-are-we-stranded-here and salmon parameters
Entering edit mode
3 months ago
pubsurfted ▴ 40

Hello. Can anyone explain to me what they mean by "a corresponding gtf" and where do I get it from? I'm super new to this stuff and have trouble understanding which files are which.

It also requires a transcriptome annotation (.fasta file - e.g. ensembl’s .cdna.fasta, or a prebuilt kallisto index), and a corresponding gtf.

And for salmon, in the following command:

salmon quant -i <transcriptome index> --libType A \
             -o <out dir and prefix> -1 test_1.fq.gz -2 test_2.fq.gz
             -p <assigned threads>

Where do I get a transcriptome index for a SRPxxxxx?

Edit: I'm working with RNA-Seq data

RNA-Seq • 255 views
Entering edit mode
3 months ago
dsull ★ 4.0k

download fasta and gtf here (if working with human): https://uswest.ensembl.org/Homo_sapiens/Info/Index

You can't use kallisto or salmon unless you build an index for them and typically an index requires a FASTA (e.g. one you'd download from the link above). The "getting started" tutorials for either tool shows you how to build an index.


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