Colin Davenport

Ok, your hunch seems to be accurate: ``` /bwa-mem2-2.0_x64-linux$ ./bwa-mem2 Usage: bwa-mem2 Commands: index create index mem alignment version print version number ...bwa-mem2/bwa-mem2-2.0_x64-linux$ bwa-mem2 ERROR: prefix is too long! /mnt/ngsnfs/tools/bwa-mem2/bwa-mem2-2.0_x64-linux$...

There has been a lot of work done on this already in the past year (see the several issues and long conversations). It has been resolved by read colouring and...

So JB 1.11.6 lets you colour according to the XS tag which is output by Tophat. Sadly this is not output by the popular STAR aligner (at least for stranded...

Hi Colin, thanks, the 'reverse template' does the job extremely nicely with paired end strand specific data aligned by STAR. That's very useful information and a nice implementation. However I...

I second this feature request! Thanks, Colin

How did you read in the GFF3 ? If you used the bioperl parser (bin/flatfile-to-json.pl) I would guess enhancer is not being picked up. One possible workaround is using all...

I am also pretty sure something, probably JBrowse, had been overwriting configured passwords in my .htaccess files. I.e. password restrictions were removed .... My workaround is a daily cron-job copying...

Identifiers would be great. These are necessary for pathway analysis, eg. in the R/Shiny Single Cell Toolkit.

Good to know, this was exactly the question I was about to pose. Thanks

If you've got a modified bam file from megalodon, you can use this tool to extract other modified motifs AFAIK https://github.com/epi2me-labs/modbam2bed