FAQ

For instructions on using deepTools 2.0 or newer, please go here. This page only applies to deepTools 1.5

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?
• [Why does the maximum value in the heatmap not equal the maximum value in the matrix?] (https://github.com/fidelram/deepTools/wiki/General-deepTools-FAQs#hm_scaling)
• How can I increase the resolution of the heatmap?
• How can I change the automatic labels of the clusters in a kmeans clustered heatmap?
• How can I manually specify several groups of regions (instead of clustering)?

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.