Kennedi Todd

mitochondrial genes

1

Is there no mitochondrial chromosome or mitochondrial gene annotation in [chm13v2.0.fa.gz](https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/analysis_set/chm13v2.0.fa.gz) and [chm13v2.0_RefSeq_Liftoff_v5.1.gff3.gz](https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/annotation/chm13v2.0_RefSeq_Liftoff_v5.1.gff3.gz)? I see you mentioned it briefly in #51 but the link does not work for me.

Is there a way to create a plot with shortened gaps that still shows exon vs CDS regions?

coloring individual nodes

2

Hello, Can you show example code for selecting individual colors for nodes? The documentation has changed since the examples shown in other issues like #20 . I have tried reading...

lima ERROR: [pbcopper] alarm ERROR: cannot write to empty alarm filename

11

Hello, I am using the command line version of smrtlink 13.1. I have a sample prepped for Iso-Seq using SMRTbell prep kit 3.0. I was given the barcodes used by...

Cannot install ComplexHeatmap

1

Hello, I am having trouble installing ComplexHeatmap and cannot load countToFPKM. It looks like it downloads ComplexHeatmap only as a binary.