Filtering Variants In Rna-Seq Data

Question

[siyu]

How can I use the RNA-seq data to filter the variants I found in the whole_genomic sequencing data,in order to confirm the variants have expressed in the cell? what tools should I use ? And the detailed steps? Thanks very much !

[Michael]

Please revise the question. First, we need more details about your biological question, organism and data, and you should give some citations of papers you have already read to show you did your homework.

Answer 1

[Sean Davis]

You will need to write your own tools to do this, most likely. There are at least two levels of detail that you will want.

1. The gene/transcript level expression
2. The allelic ratio of the variant

For #1 above, standard RNA-seq processing will get you counts (or RPKM or FPKM, etc.). I'll assume that you can work with RNA-seq data using one of the available packages. If not, there is some homework to be done.

For #2, tools like samtools mpileup or a SAM/BAM API for python, perl, java may be needed. Getting the fraction of variant alleles at each genomic location should tell you (approximately) the allele-specific expression.