Steven Wingett

Q: calculating the genome size needed for the MACS --gsize option

4

Hi, I had a query about calculating the genome size needed for the MACS --gsize option. **Use case** I shall be using genomes not listed in your documentation and so...

I recently opened a GitHub issue for the nf-core chipseq pipeline. This potential problem applies to atacseq pipeline as well. The issue regards the choice of genome size specified with...

Hi, I have been using your excellent NucleoATAC tool, but I wanted to check I have been using the output correctly. I need to assess nucleosome occupancy between different samples....

Hi, I’m a researcher at the LMB in Cambridge and we are interested in running your neuronal differentiation prediction model on additional datasets. The Jupyter notebook is fine to run,...

Processing very long reads

2

Devise a way to handle very long reads (e.g. Oxford Nanopore). Maybe make compatible with Minimap2 - as discussed by email with users. Alternatively, break up reads and process with...

rRNA genome

6

Create a rRNA genome for download (--get_genomes)that comprises multiple species and document this in the config file.

The message below could be more elegant: (base) ultraviolet@ultraviolet-X555QA:~$ fastq_screen_v0.13.0/fastq_screen fsq_test_dataset.fastq.gz Using fastq_screen v0.13.0 Reading configuration from '/home/ultraviolet/fastq_screen_v0.13.0/fastq_screen.conf' Aligner (--aligner) not specified, but Bowtie2 path and index files found: mapping...

Create a DockerHub container

4

Make FastQ Screen available on DockerHub

Make FastQ Screen Compatible with FASTA Files

HiCUP output if Tidyverse, Plotly and/or Pandoc not installed

7

HiCUP does not give nice output if HTML summary reports are not generated owing to lack of Tidyverse, Plotly and/or Pandoc. Make this more elegant.