Hi

I am using the following commands to run tximport

txi <- tximport(files, type="salmon", tx2gene=tx2gene,ignoreTxVersion=TRUE,dropInfReps=TRUE)

my tx2gene dataframe looks like this

             tx_id            gene_id
1 ENSMUST00000082387 ENSMUSG00000064336
2 ENSMUST00000179436 ENSMUSG00000095742
3 ENSMUST00000082388 ENSMUSG00000064337
4 ENSMUST00000177695 ENSMUSG00000094121
5 ENSMUST00000082389 ENSMUSG00000064338
6 ENSMUST00000082390 ENSMUSG00000064339
>

My question is which among

summarizing abundance
summarizing counts
summarizing length

contains the TPM value from the individual quant.sf files. My other question is since the txi$abundance contains the gene ids how can I get the transcript names so that I can cross check the values in quant.sf files, to see everything is running fine.

Thanks

Tanya

Check out the help page ?tximport

You can use txOut=TRUE to get out the transcript-level quantifications

The abundance list item contains the summarized abundance measurements. If you wanted to do some spot checking, you could do

listmap <- split(tx2gene$tx_id, tx2gene$gene_id)

If I do that with a tx2gene data.frame I have handy, I get

> split(tx2gene$REFSEQ, tx2gene$ENTREZID)[1:5]
$`100135779`
[1] "NM_001126230.1"

$`100136349`
[1] "NM_001123523.1"

$`100136351`
[1] "NM_001123524.1"

$`100136352`
[1] "NM_001123525.1" "XM_014194536.1" "XM_014194537.1"

$`100136353`
[1] "NM_001123526.1"

And you can see that for example Entrez Gene ID 100136352 has three transcripts that are being summarized to generate a gene level abundance. You can then look for those rows of the data from the quant.sf file and sum by hand.

Thanks James

It worked for me.