Tobias Rausch

Thanks for the suggestion! MultiQC support would certainly be useful and I'll keep it in mind, but I'm afraid this won't be a quick addition given the current workload.

Possibly some firewall issue. Maybe this helps: [https://stackoverflow.com/questions/5755819/lost-connection-to-mysql-server-at-reading-initial-communication-packet-syste](https://stackoverflow.com/questions/5755819/lost-connection-to-mysql-server-at-reading-initial-communication-packet-syste)

These files are part of the [data download](https://github.com/tobiasrausch/vc#installation---linux).

Alfred currently outputs raw gene counts or FPKMs using the `alfred count_rna` subcommand. You can convert FPKM to TPM for gene `i` using `TPM(i) = ( FPKM(i) / sum (...

Maybe the region doesn't exist? The output file should be just plot1.png. Here is a minimal example to see if the plotting using docker works for you: ```` cd /tmp/...

That's difficult to debug remotely. The region plotting and docker container look fine to me so I suspect it's a problem with the BAM file. Here is a small example...

Tracy requires boost and some other packages that you can install via brew: `brew install cmake zlib readline xz bzip2 gsl libtool pkg-config boost autoconf`

Is there any reason why you don't want to use the pre-computed GRCh38 mappability map? You can download it [here](https://gear.embl.de/data/delly/). The procedure to generate an indexed mappability map is described...

Hmm, sounds like a bug. I suspect this might be related to some small chromosomes where delly does not find enough mappable positions. Can you try removing small contigs

Closing this because it's probably very outdated. Please reopen if necessary.