deepTools
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deeptools
Tools to process and analyze deep sequencing data.
I see your proposed workaround for #907 However, I'd like to chime in on the how useful having the option to NOT merge such bins would be to an ATAC-Seq...
I have some problems about the alignmentsieve output bamfile. In the source code of **alignmentSieve.py**,I find the output mode was "wbu",why the output bam was uncompressed ?The uncompressed bam would...
Dear all, I am plotting WGBS data over predefined regions. This is command I used: ``` computeMatrix reference-point -R regions.bed \ -S DNA_3.bw \ DNA_4.bw \ DNA_1.bw \ DNA_2.bw \...
Hi, I'm using bamCoverage to generate Bigwig output. When I use samFlagExclude on full Bam alignment (strand + and -), I have different result than use BamCoverage on only one...
Hello. I'm finding that plotHeatmap is more useful for heatmaps than the "heatmap" option in plotProfile. But plotHeatmap has one big problem: it prints ALL the heatmaps in one row!...
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I have sample groups that I'd like to cluster. If my samples are 1-10 and every 2 are the same species/tissue/whatever, can I do something like --clusterUsingSamples (1 2) (3...
I am struggling to get computeMatrix to complete. It worked fine with a set of bed files for individual chromosome regions, with 95 single region beds that look like this:...
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It is slow when the numebr of bam files increases. (It could potentially be affected by the high depth of sequencing as well.)
