Question: 'Sampling' Bam or BigWig files?
gravatar for david.leader
20 months ago by
david.leader10 wrote:

I am involved in an RNAseq project in which mutliple tissues of an organism are being analysed. Normally the company doing the analysis runs between two and five lanes of each biological replicate and, after examining the appearance of the BigWig files on the UCSC browser I choose two to merge and work up through the Tuxedo pipeline and one to display on a customized UCSC browser view of tracks. Especially for BigWig, this results in comparable tracks of a managable size.

A recent tissue sample was only run on a single lane, but the fast.qz files I received were 5-10x larger than normal, as were the resulting Bam and BigWig files. Is there a program that would allow me to take a representative 'sample' from these files (e.g. one fifth) to avoid having to load a very large file on the UCSC browser?

rna-seq • 834 views
ADD COMMENTlink modified 20 months ago by Jennifer Hillman Jackson25k • written 20 months ago by david.leader10
gravatar for Jennifer Hillman Jackson
20 months ago by
United States
Jennifer Hillman Jackson25k wrote:


The tool Picard > Downsample SAM/BAM could be used. Other tools in the group SAMtools and BAMtools perform more specific filtering. One example is SAMtools > Slice BAM by genomic regions.

However, this may not be necessary. If you just want to visualize the bigWig data at UCSC, know that these files are hosted externally from Galaxy to UCSC when using the links provided in Galaxy, and only the portion of the data used in the current display window (at UCSC) are transferred over. If you haven't tried this yet please do.

Hopefully one of these options works for you! Jen, Galaxy team

ADD COMMENTlink written 20 months ago by Jennifer Hillman Jackson25k

Many thanks Jennifer for the prompt and helpful reply. I really appreciate it.

I downloaded the Picard tools and downsized the acceptedhits.bam file to 20% using DownsampleSam; ran bam_to_bigwig, and compared the profiles before and after on the UCSC browser. Absolutely fine.

(I have to use my own setup for the bigwig files because it is linked to my own web application, making the results available on-line).

ADD REPLYlink modified 20 months ago • written 20 months ago by david.leader10
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