Hi.
I am currently mapping plant transcriptome reads from one cultivar to the genome of another culitvar of the same species. It has been suggested that to improve the mapping, it might be worthwhile to correct the reference genome for use with cultivar that my reads are from.
I can see how this could improve the number of reads that map to the reference. It feels like it might be a bit circular though, as if I'm taking the transcriptome from one of my samples and using that as reference for itself (and the rest of my samples). Can anyone think of why this might be bad idea?
At the moment I am using tophat and taking the resulting insertions.bed and deletions.bed, reading the files manually and then manually ineserting these into the reference genome. Is there a better way to do this?
Cheers
Ben.
I am currently mapping plant transcriptome reads from one cultivar to the genome of another culitvar of the same species. It has been suggested that to improve the mapping, it might be worthwhile to correct the reference genome for use with cultivar that my reads are from.
I can see how this could improve the number of reads that map to the reference. It feels like it might be a bit circular though, as if I'm taking the transcriptome from one of my samples and using that as reference for itself (and the rest of my samples). Can anyone think of why this might be bad idea?
At the moment I am using tophat and taking the resulting insertions.bed and deletions.bed, reading the files manually and then manually ineserting these into the reference genome. Is there a better way to do this?
Cheers
Ben.
Comment