Question: Reads detected/"spill over" on introns after using bamCoverage function from deepTools
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kdcastillo • 0 wrote:
Hello! We recently used the recent version of bamCoverage from the deepTools suite for our ribo-seq and RNA-seq bam files to generate bigwig files. The conversions ran smoothly, however when we loaded the bigwig files into IGV, we noticed some reads spilling over to some exon-intron junctions when we zoomed into each track. We believe these are not genome misannotations because the non-normalized/non-bigwig bam files don't show these junction reads. Any advice is appreciated. Thank you!
Best, Kat
Hello, it would help if you add code and screenshots to understand the problem. My first guess when it comes to local anomalies is the chosen bin size and extension parameter (-bs -e).
Thanks for the response!
Kat