pejlab / aneva-dot Goto Github PK

Dear Aneva-Dot-Team,

thank you very much for this valuable resource.

As you know, depending on the tissue and the gene there are a few gaps in the GTEX data. I wanted to give it a shot to calculate Vg estimates from own in-house RNA-Seq data we have available. Can you indicate on how exactly this could be achieved (e.g. in R), do you possibly have sample code available?

Thank you very much!

Kind regards,
Florentine

Hallo @pejminister !

Thank you for developing and sharing these useful packages! We are very new in this field, so we started by following your tutorial ( https://stephanecastel.wordpress.com/2017/02/15/how-to-generate-ase-data-with-phaser/) . We performed both phaser and phaser_gene_ae and they worked great, but once obtained all the output files, we didn’t understand which one should be used as input for ANEVADOT, since they look differently than the sample_ASE data you shown here https://rdrr.io/github/PejLab/ANEVA-DOT/man/sample_ASE.html . There are other intermediate steps that we are missing?

Thanks in advance.

Hello,

I have a question about the input data for ANEVA-DOT. I obtained the ASE result from GATK ASEReadCounter and would like to use ANEVA-DOT for downstream analysis. I looked into the sample_ASE data you shown and noticed that the data format is a bit different from the ASE output from GATK ASEReadCounter. I am wondering how I should deal with the situation that multiple het-SNPs are mapped in a gene, because I don’t see duplicated geneID in the sample_ASE data. Do I sum up all the REF counts and ALT counts for the gene? Or I should pick counts from one of the SNPs?

Thanks in advance.

Hello, thank you for developing this package. I am wondering how p0 can be estimated? I noticed that the default is 0.000326, which is an average estimated from the GTEx v.7 data. Thank you.