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deweylab / RSEM

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
http://deweylab.biostat.wisc.edu/rsem/
GNU General Public License v3.0
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positive counts with ZERO effective length, FPKM and TPM #188

Open gianfilippo opened 2 years ago

gianfilippo commented 2 years ago

Hi,

I am finding some genes with ZERO effective length, but positive counts. TPM and FPKM are ZERO as well. I used two pipelines: 1) My pipeline, suing STAR and RSEM It shows a number of genes with ZERO effective length in all samples and small, non-ZERO counts in the same (not all) samples. In the present dataset, most of the ZERO effective length genes (in all samples) also have zero counts (in all samples), so I can simply remove them. Some genes have ZERO effective length in a few samples only, and then counts in the rest seem ok, although I have not looked at this systematically. What do you recommend for the genes with ZERO effective length and non-ZERO counts ?

2) NEXTFLOW RNAseq pipeline (as test), also using STAR and RSEM The NEXTFLOW RNAseq pipeline (2) shows a larger number of genes with ZERO effecitve length in all samples and even relatively large non-ZERO counts in the same (not all) samples (see below). ENSG00000199631.1 ENST00000362761.1 85.00 0.00 208.93 0.00 0.00

Could you please recommend how to deal with this ?

Thanks