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Hello All,
I have a question about how others are handling sequence feature versions.
I have a group that is developing gene/mRNA models. They are using an ensembl like system for versioning of …
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Hello,
I got stuck at the combine bit. I am not sure of what inputs to use for the reconstructed genome (-g) and the repeats (-r) here. I have ran so many trials but I keep getting 0 repeats to reco…
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This SEP proposes a systematic set of "stem-top" glyphs representing small sites affecting DNA, RNA, or protein. The glyphs in this system are Biopolymer Location, Stability Element, and Cleavage Sit…
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using full (even sites-only) VCFs for BQSR is heavy, especially in spark, when we broadcast them. They can go > 10GB in size. Really, it's just a few million positions, so we could compress it hugely:…
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Hi,
I'm trying to analyze our RNAseq data with GRIDSS.
I started from a trial on single bam file with a small proportion of the reference genome (chromosome 1).
The settings are as follows:
`N…
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I don't think it is possible, but I wanted to change some parameters in my simulated reads, to test different factors. One of the parameters I really want to change is the read length like max, averag…
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It looks like you are using mounted volumes for storing large files (e.g. reference genomes) on the batch job containers. I see that you are using `docker_scratch` volumes in the cloudformation YAML, …
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The curators of Malaria Parasite Metabolic Pathways (http://mpmp.huji.ac.il/) and RMgmDB (Rodent Malaria genetically modified Parasites) (https://www.pberghei.eu/index.php) would like to have links to…
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Hello,
As recommended in https://github.com/bcbio/bcbio-nextgen/issues/2689#issuecomment-465955157, I tried using GATK4 with CWL (Cromwell) for calling variants, using the population calling method…
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In tomcat 8.5 / production a target like this:
/apollo/annotator/loadLink?loc=scf7180000302113:425429..426136&usda=[gov/apollo/Drosophila%20biarmipes/jbrowse/?loc:scf7180000302113:425429..42613…