Steven Wingett comments

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                                            Steven Wingett

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Create a DockerHub container

Ah yes. I seem to remember you may need to install GD libraries on your operating system in such instances. If you Google this you should get some advice on...

fastq_screen does not yield non-zero exit code when aligner returns non-zero exit code

Thanks for letting me know. I'll look into ways to make FastQ Screen fail more elegantly when necessary. This fix should be incorporated into the next update.

Update documentation

Also, add HiCUP logo back to read the docs pages.

Update documentation

Hi, Thanks for letting me know. I'll do this in the next HiCUP release. All the best, Steven

Truncation at very start of sequence.

Hi Stephen, I trust all is going well at Bath. You are correct that since in either case this will generate short reads it will not affect the results. But...

rRNA genome

Hi, Thanks for your message. I believe it is indeed only mouse sequences. I intend to add to this list rRNA sequences from other species (human etc.) and then users...

rRNA genome

Hi, Thanks for that, however I think we need to keep tRNA separate from rRNA. Also when adding new genomes it would be best if we added the latest genome...

rRNA genome

Great, thanks. When I get a collection together I'll upload to the public downloads folder. In the meantime, users can put together their own rRNA index files. All the best,...

The pipeline has three additional scripts: hicup_combiner – this splits reads at the truncation sequence and creates new virtual read pairs hicup_allocater – this allocates reads to “their” restriction fragment...