FAQ

Here, we are collecting issues we have encountered over the time. Feel free to contribute your questions via deeptools@googlegroups.com

General deepTools-related questions

• How does deepTools handle data from paired-end sequencing?
• I just want to try out a tool, how can I optimize the computation time?
• Does it speed up the computation if I limit bamCorrelate to one chromosome, but keep the same numbers and sizes of sampling bins?
• When should I exclude regions from computeGCbias?
• When should I use bamCoverage, when bamCompare?

Heatmapper

• How does computeMatrix handle overlapping genome regions?
• How can I increase the resolution of the heatmap?
• How can I change the automatic labels of the clusters in a kmeans clustered heatmap?

External data

• What do I have to pay attention to when working with a draft version of a genome?
• How do I calculate the effective genome size for an organism that's not in your list?
• Where can I download the 2bit genome files required for computeGCbias?

Galaxy-related questions

• I've reached my quota - what can I do to save some space?
• Copying from one history to another doesn't work for me - the data set simply doesn't show up in the target history!
• How can I use a published workflow within deepTools Galaxy?
• I would like to use one of your workflows - not in the deepTools Galaxy, but in the local Galaxy instance provided by my institute. Is that possible?
• How can I have a look at the continuous read coverages from bigWig files? Which Genome Browser do you recommend?
• What is the best way to integrate the deepTools results with other downstream analyses (outside of Galaxy)?
• How can I determine basic parameters of a BAM file?

Go to the general Galaxy help page

For more information on the individual tools, see the detailed descriptions.