Dealing with multispecies using tximport about tximport

[mikelove]

I would just pretend that the extra transcripts are from the same species, and import one long count table with tximport.

The question becomes, what are you going to do next? Are you aiming to compare alleles?

NumReads is the number of reads Salmon assigned to that particular transcript. The sum of NumReads will be the number of reads Salmon could map (it doesn't add or remove reads, just fractionally proportions them).

[FlorianRocher]

Hi,

Thanks for your fast answer !
Next I will do DE analysis per species (I am dealing with a plant facing two different pathogen species). So just to be sure I understood correctly what numReads represent : Numreads is a count that was estimated from unique and multi-mappers and takes into account the size of the transcript but does not take into account the library size. Am I correct ?

[mikelove]

NumReads does not take into account transcript size, that information is the effective length of the transcript. NumReads / length = something proportional to TPM.

The sum of NumReads over the transcripts is the mapped read count. The sum of the TPM is 1e6.

[FlorianRocher]

Hi,

Alright, I get it.
Thank you for your time and all those insights !

Have a nice day

Florian