Ben Berman

Automatic CV annotator?

1

Has anyone used this to write a tool to parse and annotate PDF CVs, with the number of Scholar citations? That would be very useful! Kind of hard to do...

extendReads not properly extending short insert paired reads ...

10

I am using deeptools bamCoverage to analyze short (35-80bp) paired end fragments. All reads in my bam file are properly paired based on samtools flagstat and Picard. Yet bamCoverage extends...

Add metadata to BAM files

1

We are using the Megalodon BAM files as our primary data output for data availability. BAM files produced by most aligners typically contain `@PG` tags which give the software versions...

## Is your feature request related to a problem? Please describe We have a multi-GPU server where each process can only access a single GPU. So it is very advantageous...

This is my first time trying to use this package, which seems very useful for pulling out reads from a specific region ("-L"). However, for most of my applications I'm...

Nanoplot output files clobber each other ..

6

### Description of the bug When I run 4 samples, I only get one version of the nanoplot output files. It looks like the nanoplot module should use the --prefix...

When I associate a `--params-file` with a pipeline, it gets stored as `paramsText`. Then if I launch that pipeline with a `--params-file` it seems to overwrite the `paramsText`, when what...

there are different levels of parameters, for instance (1) algorithm settings like `min_q` and (2) `input` samplesheet and `outdir` . Therefore , it would be nice to be able to...

I believe the way bamtools random works is to first randomly pick a reference, and then randomly pick a position within the reference. For instance, in human GRCh38 , there...

Best to use a version that doesn't contain ALT chromosomes.