Hello everyone, I started to work on variant calling from RNA-Seq data. As I understood from the papers and messages I read, using RNA-Seq is a challange due to high noise in RNA-Seq data. I tried GATK4 pipeline (even it is said that the pipeline is for germline mutations) they posted in website as a tutorial on a random RNA-Seq sample FASTQ. Apperently I have variants and I annotated them with Annovar.
But the point is; as you know RNA-Seq experiments can be done as whole transcript, 3'-read etc. (I am not really familiar with experimental techniques since I do not have any laboratory experience). So basically, if a only a part of transcript is sequenced, we will miss the variants from the unread part.
Is this experimental techniques make any difference in the bioinformatics context? Is same pipeline (if anyone have another way they recommend, I would be grateful) works for all kinds of RNA-Seq? (paired data of course)
Thank you in advance