Questions about Isovar

[iskandr]

Email from Wenhui Li:

Here I have some more questions about isovar:

1. How to know the allele-specific expression of a variance? Is that "alt_reads_supporting_protein_sequence" shows the expression? Or is there any optional parameter to set to tell isovar output the Expression information (such as RPKM, FPKM or TPM)?

2. The reference fasta we used is RefSeq Gene hg19. When I run isovar, the parameter " --genome GRCh37" (the reference is Ensemble). Is that a problem? How to set this parameter of reference genome?

Thank you very much! Looking forward to your reply.

Ms. Wenhui Li

Bioinformatics Analyst in BGI, Shenzhen, China