Hi all.
I have a question about duplicated genes which have several copies in the genome such as Ccl21c. Tophat was used to map the RNA-Seq reads back to the genome and HTSeq was used to count the reads map to each gene. All of the reads stem from the duplicated genes will be get rid of by HTSeq because they are aligned to multiple places. Is there anyway to quantify these genes? Or could I mask the genomic regions of duplicated genes before running Tophat?
Any suggestion will be much appreciated.
Best
I have a question about duplicated genes which have several copies in the genome such as Ccl21c. Tophat was used to map the RNA-Seq reads back to the genome and HTSeq was used to count the reads map to each gene. All of the reads stem from the duplicated genes will be get rid of by HTSeq because they are aligned to multiple places. Is there anyway to quantify these genes? Or could I mask the genomic regions of duplicated genes before running Tophat?
Any suggestion will be much appreciated.
Best
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