read count normalization

Question

[Liftedkris]

dear all

i ran RNA-seq with 28 samples i got from GEO with the accession number GSE55648. i used HTseq to obtain the gene ensebl IDs and the read counts. now i need to normalize it to TPM but my major problem is that i have never used R. is there another way tonormalize these read counts without going through the R?

thanks liftedkris

Answer 1

[Kevin Blighe]

If you have no skills in R and are not in a position to learn, then you can use Galaxy to normalise your HTseq raw count files, by uploading them either individually or as a single count matrix file that includes the raw counts over all samples.

If you then want TPM, I would use EdgeR, as it can transform normalised counts to TPM.

Go to:

1. https://usegalaxy.eu/
2. RNA analysis (at left)
3. edgeR

Kevin