Comments (4)
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).
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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 ?
from tximport.
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.
from tximport.
Hi,
Alright, I get it.
Thank you for your time and all those insights !
Have a nice day
Florian
from tximport.
Related Issues (20)
- Outdated vignette? HOT 1
- Move Alevin import code to C++ HOT 3
- Missing release tags HOT 1
- Add option to import only whitelisted barcodes from alevin HOT 2
- ignoreAfterBar does not apply with txOut=T and countsFromAbundance != "no" HOT 1
- lose transcript names for salmon inferential replicates
- `ignoreAfterBar` not used if `txOut=TRUE` HOT 5
- cann't import kallisto abundance.h5/.tsv HOT 4
- Import processed data HOT 3
- Recomended count scaling method for DTU analysis HOT 2
- Returns TPM when abundanceCol is set to any value for type='rsem' HOT 1
- Read in files in parallel HOT 4
- Tximport issue with new R version HOT 2
- Which measure to use for gene Fold change analysis between pre- and post-treatment samples and for gene comparison within a sample HOT 1
- error in 1:nrow(m): argument of length 0 HOT 1
- import using tximport for the rsem count table to get integers? HOT 3
- Different length and counts depending on the number of loaded samples HOT 1
- tximport of feature counts? HOT 1
- tximport of kallisto h5s generated with multiple threads is not deterministic HOT 1
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