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!
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!
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