Question: Gene level from transcript level expression estimate.
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gravatar for mforde84
16 months ago by
mforde841.2k
mforde841.2k wrote:

Would it be appropriate to simply sum FPKM/RPKM/TPM normalized data across transcripts to generate a gene level estimate? Each transcript will be abundant at a certain % of total expression, so the intergration should simply be the gene level expression of all associated transcripts. Am I correct or am I missing something?

rna-seq • 817 views
ADD COMMENTlink modified 16 months ago by eu.sanisa0 • written 16 months ago by mforde841.2k

I'd think the answer is no, depending on how 'gene level estimate' defined. Since transcripts associated with a gene can share exons, I'd think summing counts including overlapping transcripts from the same gene would lead to multiple counting. Or did you mean summing reads over all exons associated with a gene locus?

ADD REPLYlink written 16 months ago by Ahill1.4k
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gravatar for eu.sanisa
16 months ago by
eu.sanisa0
eu.sanisa0 wrote:

If by transcripts you mean isoforms, then i think it is ok. I was wondering the same so i took a look at Trinity's align_and_estimate_abundance.pl . There is an option to give a "transcripts to gene map" and obtain a count matrix at the gene level. As I understand from the script, this uses either kallisto_trans_to_gene_results.pl or eXpress_trans_to_gene_results.pl . This last one has the statement: "compute it based on the formula: FPKM_gene = FPKM_isoA + FPKM_IsoB + ... "

ADD COMMENTlink written 16 months ago by eu.sanisa0
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