Meaning of columns in TSV Kallisto mapped file

Question

[Antonio R. Franco]

I've been using the abundance.tsv files found after mapping with kallisto.

You see 4 different columns but I am sort of confused about the actual values shown in these columns

Can somebody enlight me?. I cannot find details on how these values are calculated in the Kallisto manual

In particular.. I highlighted column TCONS_00016022. How can it be possible to have a value of TPM of 754064 when only 45 est_counts have been estimated ? The length of the gene is not that different when compared to other genes

Answer 1

[Antonio R. Franco]

Shame on me.

After the latest update of LibreOffice, it does not handle the "." and the "," as before.

I am spanish, and the "." are not meaning decimals. For that, we use colon ",".

But in any case, LibreOffice is not doing a nice job anyway. If found 43.663, it converted to 43663. But after finding 49.3074, it leaves it as is

I keep the message live to alert to other colleagues.

[GenoMax]

, is a comma. A colon is :. Just so there is no further confusion.

After the latest update of LibreOffice, it does not handle the "." and the "," as before.

Is that due to your locale/language not being set properly after the update?

Answer 2

[ATpoint]

I would first of all make sure this is not an Excel artifact by grep-ing it in the original file. These values are absurdly high.