Chris Keeling

Some clusters have more than one protein with equal longest length, but only one is chosen as the cluster representative. How does cd-hit choose THE representative when there are more...

Hi @KatharinaHoff @tomasbruna I am encountering a similar problem, except without seeing the segmentation fault, using the following command: ```bash braker.pl --genome genome.fa --UTR=on --stranded=+,- --bam=merged_fwd.bam,merged_rev.bam --softmasking --cores 48 ```...

Hi @LarsGab and @KatharinaHoff I am experiencing a similar error when using the augustus.hints.gtf or the tsebra.gtf when combining protein and RNAseq augustus.hints.gtf files. It seems that these files do...

Hi @cfarkas @LarsGab and @KatharinaHoff If you add the gene_id and transcript_id tags as indicated in my comment above, gffread should not give you errors. I wrote the following little...

This seems to be a problem with GeMoMa (GeMoMa-1.6.2.jar) that is described elsewhere: [https://github.com/Jstacs/Jstacs/issues/12](https://github.com/Jstacs/Jstacs/issues/12) and [https://github.com/Gaius-Augustus/GUSHR/issues/2](https://github.com/Gaius-Augustus/GUSHR/issues/2). I am running BRAKER in a Singularity container, and thus GeMoMa.ini.xml cannot be written...

Hello @sanyalab, When I build the container, it pulls the most recent versions of most things. But, on singularity hub, the container is stored already built, so it is frozen...

Thanks @sneumann, the pdf link is broken but @yguitton is now aware of this, and directed me to additional information, including [metaMS](https://github.com/yguitton/metaMS) and the [metaRbolomics Toolbox](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6835268/).

> ...I repeated the test and installed the last XCMS version from GitHub after updating Matrix and now it seems fine... Thanks for this info @rickhelmus -- I just had...

Hello @sneumann and @jorainer I'm trying to understand the version numbers for xcms on GitHub versus BioConductor. Currently, if I install from GitHub with `githubinstall("xcms")`, it is version xcms_3.21.3, but...

Sorry @jorainer for not following up on this. I found that IPO was having other issues that prompted me to stop trying to use IPO altogether, and thus I could...