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Example workflows
friedue edited this page Jan 17, 2014
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A collection of issues we have encountered over the time. Feel free to contribute your questions, most notably via deeptools@googlegroups.com
- 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?
- 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?
- 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 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?
For more information on the individual tools, see the detailed descriptions
deepTools is developed by the Bioinformatics Facility at the Max Planck Institute for Immunobiology and Epigenetics, Freiburg. For troubleshooting, see our FAQ and get in touch: deeptools@googlegroups.com
Wiki Start Page | Code | deepTools Galaxy | FAQ | Glossary | Gallery |
WIKI-START > Example workflows
- I have downloaded/received a BAM file - how do I generate a file I can look at in a Genome Browser?
- How can I assess the reproducibility of my sequencing replicates?
- How do I know whether my sample is GC biased? And if yes, how do I correct for it?
- How do I get an input-normalized ChIP-seq coverage file?
- How can I compare the ChIP strength for different ChIP experiments?
- How do I get a (clustered) heatmap of sequencing-depth-normalized read coverages around the transcription start site of all genes?
- How can I compare the average signal for X- and autosomal genes for 2 or more different sequencing experiments