read count normalization
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
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Kevin Blighe
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Liftedkris •
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Liftedkris •
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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:
- https://usegalaxy.eu/
- RNA analysis (at left)
- edgeR
Kevin
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