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Question: Plot normalized coverage across genes/transcripts in single cell rna seq data
1
gravatar for kevin.stachelek
10 days ago by
kevin.stachelek • 10
kevin.stachelek • 10 wrote:

I'd like to generate a plot similar to the included image. What is the name of such a plot and does there exist a simple tool to generate, preferably compatible with multiqc and/or R/bioconductor?

enter image description here
rna-seq single cell R • 67 views
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modified 10 days ago by kristoffer.vittingseerup • 2.9k • written 10 days ago by kevin.stachelek • 10
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gravatar for kristoffer.vittingseerup
10 days ago by
kristoffer.vittingseerup • 2.9k
European Union
kristoffer.vittingseerup • 2.9k wrote:

Maybe CoverageView? Looks like it was made for other experiment types but since it uses bam files as input it might work. Else Bioconductors bamsignals have a bamCoverage() function

Else I know RSeQC have a gene-coverage tool which you can find here.

Just be aware that generally in single cell data (especially for 5' end data such as 10X) you have way to few reads per gene to look at coverage. Most genes have very few reads so how much sense it makes to calculate this I'm note sure.
ADD COMMENT • link written 10 days ago by kristoffer.vittingseerup • 2.9k

thanks. I'm working with Smart-seq data so I hope I have enough reads to make an intelligible plot.

ADD REPLY • link written 5 days ago by kevin.stachelek • 10
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