Question: When displaying a BAM file in the UCSC browser, will all the data be shown?
gravatar for Jason
4.5 years ago by
United States
Jason30 wrote:

I have recently mapped RNA-seq reads to the sacCer2 genome using bowtie in galaxy. I then filtered the SAM file for reads that mapped. Then I converted to bam and clicked the link to visualize in the UCSC browser. My question is will every single read be displayed in the UCSC browser or does it randomly select a certain percentage of reads to visualize? I ask because sometimes it looks like there are fewer reads than expected based upon a separate calculation of how many reads should overlap with a given gene. When there is a small enough number that I can count it appears to match up but when it's more than 50 reads it looks like some reads are being left out. 


rna-seq bam ucsc browser • 1.7k views
ADD COMMENTlink modified 4.5 years ago by Bjoern Gruening5.1k • written 4.5 years ago by Jason30
gravatar for Bjoern Gruening
4.5 years ago by
Bjoern Gruening5.1k
Bjoern Gruening5.1k wrote:

Hi Jason,

I'm not aware of any filtering of BAM files on the UCSC site. But best practise is to convert your BAM file to bigWig before displaying at UCSC. This conversion can be done by several tools, for example bamCoverage from deepTools.



ADD COMMENTlink written 4.5 years ago by Bjoern Gruening5.1k
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