Getting gene counts from transcript counts using R package 'tximport'

Question

[arsala521]

Hi everyone,

I am working with RNA-seq data analysis. I want to convert transcript counts to gene counts. I have estimate counts of transcript using Kallisto and I want to use tximport R package to get counts for gene instead of transcripts.

Basically, I have an input tsv file like this:

ENST00000431440.2       0
ENST00000390583.1       1
ENST00000390584.1       5.5
ENST00000390585.1       2.5
ENST00000430425.1       0

and I want the output with gene ids in the first column and their counts in the 2nd column.

From the vignettes page of tximport R package here: (https://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html#kallisto), I very much got how to do this task using tximport but I am not understanding how to prepare the input object. I got that I have to use this:

txi.kallisto <- tximport(files, type = "kallisto", tx2gene = tx2gene, ignoreAfterBar = TRUE)

but what is files in this command and how can I prepare this input object in my situation. If someone can please help me with this.

TIA

[sansan96]

This works for me, maybe you can try it:

###Locate the directory containing files generated by kallisto
base_directory <- "C:/Users/kallisto_quantification"
dirs <- list.files(base_directory)

###Create a vector 
quant_files <- list.files(base_directory, pattern = "abundance.tsv", recursive = TRUE, full.names = TRUE)

### Check the files
quant_files

### Verify that the files exist
all(file.exists(quant_files))

###
gtf_file <- "example.gtf"

### Check that the file exists
file.exists(gtf_file)

### Create a transcripts database using the GTF file with GenomicFeatures
txdb <- makeTxDbFromGFF(gtf_file)

###
keytypes(txdb)
columns(txdb)

###
k <- keys(txdb, keytype="TXNAME")
tx_map <- select(txdb, keys = k, columns="GENEID", keytype = "TXNAME")
head(tx_map)

### Save the tx2gene
tx2gene <- tx_map
write.csv(tx2gene, file = "tx2gene.csv", row.names = FALSE, quote = FALSE)
txi <- tximport(quant_files, type = "kallisto", tx2gene = tx2gene)

Answer 1

[jv]

files for tximport should be a character vector of filenames for the transcript-level abundances (as described in the function documentation/usage), i.e.

files <- c("sample_1.abundance.tsv", "sample_2.abundance.tsv")

One easy option is to have all of the abundance.tsv files in a directory and use list.files to read all the filenames into a vector.

[arsala521]

Got it. Thank you so much. I wasn't able to catch it from vignettes page as it was written in little complicated manner and my R knowledge is very basic, not advanced. Thanks again :)

[Ram]

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