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Old 07-12-2019, 03:24 PM   #1
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Location: Israel

Join Date: May 2011
Posts: 4
Unhappy tximport problem - won't recognize when there is an isoform and throughout data

I was hoping someone can please help me with an issue I can’t really figure out…

I ran samples on Salmon through Galaxy. I also provided a conversion file, with transcript name and gene ID (C. elegans). However, when I look on the “gene quantification” output, which supposed to have “WBGene00022229” for example, many of the entries have the gene name (F54D7.7 for example). I checked and these genes are mapped in the file I provided, but they have slight modification (for example, F54D7.7.1 instead of F54D7.7).

When I ran it through tximport on RStudio, it seems like it throws out these genes because it can't find it in the table. In other words -on the transcript level these map to something that is not the exact match. However, I downloaded the data from Ensembl with the same information/version so it is not clear to me why it is different.

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galaxy, salmon, tximport

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