How to convert Kallisto output to Salmon?

Question

[from the mountains]

What's the best way to do this? I am looking to produce the salmon .sf file.

[Mensur Dlakic]

Google has quite a few suggestions.

https://www.google.com/search?q=How+to+convert+Kallisto+output+to+Salmon%3F

[from the mountains]

thanks, maybe i'm going crazy but i don't see an exact answer to the question i asked in those search results. the first result shows how to convert salmon to kallisto (the opposite) so it can be used in sleuth. the rest are how to import either kallisto or salmon into R for edgeR or tximport. As far as i can see these methods do not take the .h5 file and output the .sf file. maybe my mistake is in assuming there exists such a method that i don't have to make myself.

Answer 1

[dsull]

kallisto's abundance.tsv and salmon have basically the exact same columns (transcript, length, effective length, TPM, counts, etc.) -- why not just rename & reorder the columns?

[from the mountains]

makes sense, i didn't realize kallisto had a plaintext option. printed a plaintext option by default