Dear all
I am working on a Trascriptome project (Illumina GAIIx, paired ends).
I have 2 samples of Arabidopsis Thaliana. Within their sequences, an external sequence of a different genome has been inserted (transfection should be the word): the reason behind this choice is that we would able to identify the gene (prior unknown) that this sequence links, so that we can easily look at this gene expression.
My problem is that I need to identify which gene the sequence links.
Is there any software that achieves my goal?
I did classical RNA-seq steps:
- QC
- Alignment (Tophat - Bowtie)
- DEG (Cufflinks/diff)
I cannot search the external sequence into the aligned samples since the external sequence does not align with the samples' reference genome.
Thank you!!
Best
Andrea
I am working on a Trascriptome project (Illumina GAIIx, paired ends).
I have 2 samples of Arabidopsis Thaliana. Within their sequences, an external sequence of a different genome has been inserted (transfection should be the word): the reason behind this choice is that we would able to identify the gene (prior unknown) that this sequence links, so that we can easily look at this gene expression.
My problem is that I need to identify which gene the sequence links.
Is there any software that achieves my goal?
I did classical RNA-seq steps:
- QC
- Alignment (Tophat - Bowtie)
- DEG (Cufflinks/diff)
I cannot search the external sequence into the aligned samples since the external sequence does not align with the samples' reference genome.
Thank you!!
Best
Andrea
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