The NGS data (VCF files) contain the variants from all the transcripts for a particular gene. Which is the best site/tool to filter out all the non-primary transcripts.
Is it a RNAseq data? And what do you mean by unnecessary/non-primary transcripts?
What do you mean by non-primary transcripts? Are you looking at differential gene expression?
Sorry i should have used the term reference transcripts maybe. I am looking at DNA sequencing data for clinical diagnosis - picking up mutations. For example when i look up G6PD gene in ensemble it gives a list of 11 transcripts, 7 of which are protein coding. We use the transcript with the best TSL/APPRIS score as reference transcript. However the NGS data generated shows the same mutation from all the 7 transcripts. I am looking for a site like SNP NEXUS that can filter out the remaining six results.
Thanks
Now it's getting complicated. What sequencing did you perform, is it DNA or RNA? Analyse transcripts with DNA seq data seems not very likely. However, if you got the hit for mutation in 7 transcript from comparison to the reference, why do you want to discard all except one. Or why not manually extract the best transcript which could be better for further analysis.
Dear Abhijeet,
It's DNA. Yeah thats what we have been doing. Manually selecting the best transcript. But doing so for each patien'ts sample takes a lot of time which we find it hard to afford on the diagnostic side :-) .
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