How to get expression values for specific genomic coordiantes, not genes?
Hi people,
I'm rather new to the RNA-Seq area, so please bear with me if my question seems idiotic. I want to use the BodyMap 2.0 BAM files in order to study how certain regions of interest of the human genome vary in expression depending on the tissue. I have a set of genomic coordinates of interest that might or might not coincide with genes (most of them will not, just sporadic open reading frames) as BED files. My question is: what would be the best choice in order to build a pipeline that would lead me to expression values/number of reads for my set of coordinates? Would the standard BAM file > Cufflinks > Cuffdiff work? Could I use my BED file as template instead of the UCSC Gene Track in order to get my expression values?
Many thanks!
I'm rather new to the RNA-Seq area, so please bear with me if my question seems idiotic. I want to use the BodyMap 2.0 BAM files in order to study how certain regions of interest of the human genome vary in expression depending on the tissue. I have a set of genomic coordinates of interest that might or might not coincide with genes (most of them will not, just sporadic open reading frames) as BED files. My question is: what would be the best choice in order to build a pipeline that would lead me to expression values/number of reads for my set of coordinates? Would the standard BAM file > Cufflinks > Cuffdiff work? Could I use my BED file as template instead of the UCSC Gene Track in order to get my expression values?
Many thanks!
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