Dear seqanswers community,
I have Illumina RNAseq reads from a species hybrid of two parental species for both of which we have a draft genome. One of the reference genomes is well annotated, so I decided to first go for a reference based alignment/assembly using the tophat/Cufflinks/Cuffdiff pipeline as described in Trapnell et al. 2012 Nat. Protocols.
I got >60% of my reads mapped to either of the parental genomes, so was happy about this. And the cuffdiff results also look ok.
I was wondering though, is it possible to reconstruct the sequence from my RNAseq that mapped to the same "gene" from my reference genome?
If this was possible, I would like to assemble only those reads that show differential expression into contigs. Is there a program/tool that could use the gtf file from Cufflinks (plus the .bam from bowtie) as a guide for this?
I am new to RNAseq, so maybe someone with more experience knows about tools that could do this... I am not a great programmer, so would prefer to skip writing a script... unless there's no way around it.
thanx in advance.
I have Illumina RNAseq reads from a species hybrid of two parental species for both of which we have a draft genome. One of the reference genomes is well annotated, so I decided to first go for a reference based alignment/assembly using the tophat/Cufflinks/Cuffdiff pipeline as described in Trapnell et al. 2012 Nat. Protocols.
I got >60% of my reads mapped to either of the parental genomes, so was happy about this. And the cuffdiff results also look ok.
I was wondering though, is it possible to reconstruct the sequence from my RNAseq that mapped to the same "gene" from my reference genome?
If this was possible, I would like to assemble only those reads that show differential expression into contigs. Is there a program/tool that could use the gtf file from Cufflinks (plus the .bam from bowtie) as a guide for this?
I am new to RNAseq, so maybe someone with more experience knows about tools that could do this... I am not a great programmer, so would prefer to skip writing a script... unless there's no way around it.
thanx in advance.