Hey all. First post, sorry if it's a stupid question.
To make a long story short:
I've inherited a project in our lab working on a putative alternative splicing event of a gene. Instead of messing with wet bench experiments I decided to analyze some RNA-Seq data to determine how prevalent this isoform may be.
I've combined something like 50 SRA files and done tophat alignment. I've found every gene junction except for the one that was predicted to be alternatively spliced! The problem is that this gene is expressed at very low levels and I may not be seeing the AS version because of overall reads.
Is there something I can use that will count the total reads aligning to the gene or the number of times the other junctions have been found and give me a confidence or p-value that the AS event does NOT exist?
Essentially I need to make a mathematical decision on whether it is worth continuing this project or to maybe conduct another RNA-Seq to gain more confidence.
Thanks in advance!
Germwise
To make a long story short:
I've inherited a project in our lab working on a putative alternative splicing event of a gene. Instead of messing with wet bench experiments I decided to analyze some RNA-Seq data to determine how prevalent this isoform may be.
I've combined something like 50 SRA files and done tophat alignment. I've found every gene junction except for the one that was predicted to be alternatively spliced! The problem is that this gene is expressed at very low levels and I may not be seeing the AS version because of overall reads.
Is there something I can use that will count the total reads aligning to the gene or the number of times the other junctions have been found and give me a confidence or p-value that the AS event does NOT exist?
Essentially I need to make a mathematical decision on whether it is worth continuing this project or to maybe conduct another RNA-Seq to gain more confidence.
Thanks in advance!
Germwise
Comment