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Forum: UK - Cambridge 11-21-2018, 08:00 AM
Replies: 0
Views: 1,932
Posted By StevenW
Cambridge Bioinformatics Hackathon 2018

Babraham Bioinformatics is organising a three-day life sciences-related hackathon at The Centre for Computing History in Cambridge. The hackathon is an excellent opportunity to improve your coding...
Forum: Events / Conferences 10-12-2018, 04:16 AM
Replies: 0
Views: 951
Posted By StevenW
Exclamation The Cambridge Bioinformatics Hackathon 2018

Babraham Bioinformatics is organising a three-day life sciences-related hackathon at The Centre for Computing History in Cambridge. The hackathon is an excellent opportunity to improve your coding...
Forum: Bioinformatics 10-02-2017, 04:54 AM
Replies: 67
Views: 19,858
Posted By StevenW
FastQ Screen Bisulfite Problem

Hi jaas,

I am one of the developers of FastQ Screen. Hopefully we can get this problem resolved quickly.

Would you be able to send me the configuration file you used when running FastQ...
Forum: Bioinformatics 09-28-2015, 07:05 AM
Replies: 67
Views: 19,858
Posted By StevenW
Hi, Thanks for your message; I am part of the...

Hi,
Thanks for your message; I am part of the team responsible for developing FastQ Screen.
We removed the --paired option from the script in a recent update as we felt it was unnecessary and was...
Forum: Bioinformatics 09-07-2015, 04:42 AM
Replies: 67
Views: 19,858
Posted By StevenW
Excellent, so everything is fine? PS I'm...

Excellent, so everything is fine?

PS I'm releasing a new version of the software today.
Forum: Bioinformatics 08-20-2015, 02:39 AM
Replies: 67
Views: 19,858
Posted By StevenW
Hi, I am responsible for developing FastQ...

Hi,
I am responsible for developing FastQ Screen.

The standard way to remove contamination is:
Run FastQ Screen (latest version) with --subset (to process the entire dataset) and --nohits. In...
Forum: Bioinformatics 08-12-2014, 11:46 PM
Replies: 67
Views: 19,858
Posted By StevenW
Fastq_screen

Hi,

Glad that worked.

In paired-end mode the program writes the forward and reverse reads to two separate 'nohits' output files. The reads will be in order with respect to one another in the...
Forum: Bioinformatics 08-12-2014, 12:46 AM
Replies: 67
Views: 19,858
Posted By StevenW
No Hits Problem

Hi,

I am also responsible for developing FastQ Screen. I believe the problem is caused by the path to Bowtie2 in your configuration file being incorrect.

The Fastq Screen output states:
...
Forum: Bioinformatics 03-10-2014, 03:21 AM
Replies: 67
Views: 19,858
Posted By StevenW
Checking the number of reads is the same

Hi Nathan,

Thank you for your email. I would expect the ďnohitsĒ file to be very similar to the input file since 99.98% of the reads do not map to any genome. Just to check this is not a bug,...
Forum: Bioinformatics 07-11-2013, 02:40 AM
Replies: 67
Views: 19,858
Posted By StevenW
Hi, I’m responsible for developing...

Hi,

I’m responsible for developing fastq_screen. The path to the index should include the genome base name. Adjust the configuration file so the index paths are:...
Forum: Bioinformatics 12-12-2012, 09:16 AM
Replies: 6
Views: 4,269
Posted By StevenW
SeqMonk

Perhaps Seqmonk would be of use. SeqMonk is a program to enable the visualisation and analysis of mapped sequence data. The progam allows the user to divide the genome into sliding windows and then...
Forum: Bioinformatics 03-29-2012, 01:39 AM
Replies: 3
Views: 1,610
Posted By StevenW
Hi, I am based in the Forum. Today is fine...

Hi,

I am based in the Forum. Today is fine to discuss (morning is better).

S
Forum: Bioinformatics 03-27-2012, 04:25 AM
Replies: 3
Views: 1,610
Posted By StevenW
Hi-C User Pipeline (HiCUP)

Hi,

Iím a bioinformatician at the Babraham Institute in Cambridge, UK and Iíve just produced a pipeline (named HiCUP) for processing Hi-C sequence data.

The pipeline, comprising several Perl...
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