Hello,

I have quant.sf files from salmon output for multiple samples and I want to make TPM matrix such as:

gene file1_TPM file2_TPM ____ filen_TPM

The quant.sf files are located in a directory which has all the sample directories and each contains each quant.sf file which all have same names. I want to extract file names for TPM columns for the sample directories that contain quant.sf files. Thank you for the help!

Hi, this can be achieved via tximport. Please take a look at the example in the vignette: Importing transcript abundance with tximport: Salmon

Kevin