How to get DEPTH, as well as variant calling of transcriptome data

Question

[gskbioinfo143]

Hey for RNA-seq data analysis. how to get accurate depth, variant calling results.

any accurate practical guidelines for RNA-SEQ

THANKS

Answer 1

[Ashutosh Pandey]

Read GATK best practice workflow for variant calling using RNA-seq. It is pretty much the same workflow as variant calling using genomic data but it includes splitting of the reads with 'N' operator in the CIGAR string into individual sub-reads followed by trimming of the overhanging portions if any. The VCF file will have information about the depth along with the variant calls. See: https://www.broadinstitute.org/gatk/guide/best-practices?bpm=RNAseq

[gskbioinfo143]

Hey please help me with this questions

How to calculate size of Human Transcriptome data?

[Ashutosh Pandey]

What you mean by size here? I would strongly suggest you to look into Picard (http://broadinstitute.github.io/picard/) if your overall goal is to collect some metrics about RNA-seq data. If you need to call variants follow my answer above.

Answer 2

[Lynxoid]

You could use samtools for depth, but you have to account for the fact that genome length > transcriptome length