deepTools
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deeptools
Tools to process and analyze deep sequencing data.
Using deepTools 3.1.1, python 3.10. I am able to run computeMatrix successfully without the `--unscaled5prime` argument. However, when I use the same inputs but add `--unscaled5prime 300` no output file...
I have been unable to rotate labels 90 degrees in my plotHeatmap outputs. I've tried running with and without a variety of `--labelRotation` specifications. I've attached an example. Is there...
deeptools 3.5.1 Python 2.7.5 computeMatrix reference-point -R h3SummMerged.bed -S $h3bbws -o matrixH3.gz --outFileNameMatrix matrixH3.tsv --outFileSortedRegions sortedPeaksH3.bed --upstream 1000 --downstream 1000 --binSize 10 --blackListFileName blacklist.bed --samplesLabel $labels3b --referencePoint center plotHeatmap -m...
Hi, thanks for the amazing tools! I'm having an issue with `ComputeMatrix` when providing bigwigs generated via `bigWigMerge`. briefly, my pipeline is ``` # generate single replicate bw files [...]...
I could not find it in the Documentation. Could you please point me to an API that would perform similarly to computeMatrix + plotProfile? [(https://deeptools.readthedocs.io/en/develop/content/tools/plotProfile.html)](url)
Hi, I use bamcoverage RPKM to normalize individual samples. Now I want to compare two different chip-seq samples by visualizing them in heatmap, is RPKM normalization to each individual sample...
Does anyone know the effective Genome size of the new mouse reference? mm39 aka [GRCm39](https://www.ncbi.nlm.nih.gov/assembly/7358741)? Is it the same? Sorry if this is a dumb question.. Thank you for your...
hi，i meet a strange problem with running computematrix. `error:` > Traceback (most recent call last): > File "/share/home/fanglab/liuyu/anaconda3/envs/chip/bin/computeMatrix", line 14, in > main(args) > File "/share/home/fanglab/liuyu/anaconda3/envs/chip/lib/python3.6/site-packages/deeptools/computeMatrix.py", line 421, in main...
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I don't actually know if I have an issue yet, but I am surprised that after 30 min running this command: > alignmentSieve -b /data/gpfs-1/users/amonaco_m/project_work/projects/12_DrosophilaF1Hyb_scSeq/2_10XscATAC/6_totalCounts/Hyb2Dsec/Hyb2Dsec/outs/possorted_bam.bam --minMappingQuality 10 --filterMetrics ~/scratch/bam_storage/dsec.sieve.log.txt -o...
