Question: Plotting only intergenic reads on chromosomes?
0
3.0 years ago by
Germany/Dresden/ CRTD - DZNE
Mehmet Ilyas Cosacak0 wrote:

Hi,

I have BAM files (RNA-Seq data, 75 bp reads) from alignment to Zebrafish genome. I know how to plot all reads in the BAM file on each chromosomes, using gviz. However, I want to plot only the reads that do not map to any known Genes, (exons or introns), rRNA, tRNA, etc. Specifically I am interested in the reads that map to intergenic regions.

I have used gviz to plot all the reads, but could not find a way to plot the reads that mapped to intergenic regions. Is there an easier way or any package suggestions?

p.s. I am planing to extract reads that do not map to ENSEMBL genes (using GTF file) and then plot them on the chromosomes? Is there a way to extract those reads that do not mapped to ENSEMBL genes from the BAM files?

ilyas.

modified 2.9 years ago by Martin Morgan ♦♦ 23k • written 3.0 years ago by Mehmet Ilyas Cosacak0
3
2.9 years ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:

I think you should use GenomicAlignments::readGAlignment[Pairs]() and then query[query %outside% subject], where query are your alignments and subject the regions of interest from the GTF file.

Thanks Martin for the reply and suggestion. This only helps me to extract the reads. How can I plot them on the chromosomes? Is there any package you can suggest?

best regards,

ilyas.