Exon-Junction mapping: re-assigning CDS-mapped reads to chromosomes

[sridharacharya]

Hi,

I am working with RNA-SEQ data and want to align SOLiD reads using publicly available software. Tophat cannot handle SOLiD reads, so I am going with Bowtie. But the problem is the mapping of exon-junctions. For this, I downloaded the REF-SEQ cDNA sequences from UCSC.

So my strategy is to first use align the reads to the genome (chromosomes) and then align the remaining unmapped reads to REF-SEQ cDNA sequences. Subsequently, I want to re-assign the "REF-SEQ cDNA aligned reads" to the chromosomal sequences, so that I can use the alignments with program like Cufflinks, to find enrichment.

My question is regarding re-assigning the "REF-SEQ cDNA aligned reads" to the chromosomal sequences? Is there a tool available for this? Is there a program available apart from Cufflinks to find the enrichment of reads/compare two experiments?

Thankyou for your suggestions!

[glacerda]

There are many programas for differential expression analysis in RNA-seq data. My favorites are edgeR and DEseq. Both are R packages, but they are well documented and easy to run, even for a R begginer like me.

You should input the raw read counts to these programs, so you could sum the number of reads mapped to genome and mapped to reference transcripts, summarizing this information for each locus, without counting twice reads that map to both genome and transcript.