Get The Idea Of Splicing From Reads Mapped In Rna-Seq

Question

[antgomo]

I've got a set of 100 bam files from a public experiment, I want to have an idea of splicing in each of them regarding three exons,without entering in some kind of depth-level procedure like Cufflinks or DEXSeq,

Lets say that my exons are named 1,2 and 3, and I want to know in how many samples I have a splicing event of the number two, so i was looking in the threads and I found that using coverageBed with my bed file of the three exons I could get some kind of idea per bam file

coverageBed -split -abam my_alignment -b exons_to.bed

Am I correct?

I was also thinking of getting the reads mapped in flanking end positions of read 1 and start of read 3 with samtools

What do you think about it? Any idea will be kindly appreciated

Thanks in advance!

Answer 1

[Istvan Albert]

Use bwa mem then sort the reads by name and you can easily get reads that map across junctions.

Answer 2

[Charles Warden]

I would recommend MATS for identifying splicing events (for example, exon skipping - for exon #2 in your case, I believe):

http://rnaseq-mats.sourceforge.net/

MISO is probably a more popular option, but I think MATS is more specific (and the result table is easier to read):

http://genes.mit.edu/burgelab/miso/

If you have long and/or paired end reads, I would also recommend viewing splicing junctions with a sashimi plot in IGV

[Charles Warden]

In fact, his review has recently been published:

http://www.humgenomics.com/content/8/1/3