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twlab / TEProf2Paper

TEProf2 Pipeline used to find promoters and predict protein sequences from RNA-sequencing data
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How to filter the GTEX normal samples? #17

Open songlyzz opened 3 months ago

songlyzz commented 3 months ago

Hi nakul: Recently, I used the TEprof2 to find some interesting TE-gene chimeric transcripts. But I suspect it may happen in noramal tissue. The STEP12 write "In the case of our publication, we filtered based on presence in TCGA normal samples and GTEx normal samples in choosing the candidate transcripts." Could you please teach me how to do this step?

Sincerely, Song

nakul2234 commented 2 months ago

Hello Song,

In our study, we first obtained a reference from the TCGA data. Subsequently we used the "reference-guided" mode of the pipeline with this reference and ran the GTEx data through that. The GTEx data was aligned and assembled using the same parameters as the TCGA data. We then would get the expression of each candidate across all the GTEx samples. Then we could decide on a threshold for which ones were tumor-specific or enriched. In our case, we chose 8x enriched in presence of tumor samples versus normal samples.

Best, Nakul