deepTools
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deeptools
Tools to process and analyze deep sequencing data.
Hello! I have a series of Chip-seq results.and I add some spike-in cells in my sample to normalized my chip valuel. I calculate the scale-factor from sample mapped reads and...
**Welcome to deepTools GitHub repository! Please check the following regarding your pull request :** - [ no ] Does the PR contain new feature? - [ yes ] Does the...
Hi, I am trying to plot an plotHeatmap of multiple chip-seq signals side by side by calculating computeMatrix refernec point using multiple bed and bigwig file. can you provide an...
Greetings, I'm getting an error trying to run `bamCoverage` on a bam file (converted from bed via `bedToBam` and then sorted/indexed by `samtools`). Tech details below. Any guidance is much...
I am using deeptools bamCoverage to analyze short (35-80bp) paired end fragments. All reads in my bam file are properly paired based on samtools flagstat and Picard. Yet bamCoverage extends...
Hi, I am having a couple of issues with running GC bias correction using deeptools as part of a CNV calling pipeline. 1. The DLRS scores differ slightly when number...
I am new to deeptools and chipseq data analysis , Wanted to plot density TSS and genebody using computematrix and plotprofile, the wig file which is needed for compute matrix...
When I use deepTools computeMatrix 3.1.2 to calculate the different TF binding signal around the peaks,I meet some problem. When we extend the -a -b region from 1kb,2.5kb,5kb,10kb,25kb to 50kb...
When I plot a heatmap with specifying a Zmin value rows in the middle of the heatmap are returned as white lines. I am using Python 2.7.16 and deeptools 3.4.3....
hello I want to use computematrix Tools to DiscoverAny enrichment at a point .Such as replication start Point. Should I choose --referencePoint center？ thank you