Question: Plotting only intergenic reads on chromosomes?
0
gravatar for Mehmet Ilyas Cosacak
2.8 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?

thanks in advance.

ilyas.

ADD COMMENTlink modified 2.8 years ago by Martin Morgan ♦♦ 23k • written 2.8 years ago by Mehmet Ilyas Cosacak0
Answer: Plotting only intergenic reads on chromosomes?
3
gravatar for Martin Morgan
2.8 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.

ADD COMMENTlink written 2.8 years ago by Martin Morgan ♦♦ 23k

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.
 

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by Mehmet Ilyas Cosacak0
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