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Forum: Bioinformatics 09-10-2018, 02:25 AM
Replies: 2
Views: 457
Posted By simonandrews
If you have a look at the Differential...

If you have a look at the Differential Methylation Leture document on our methylation training course (http://www.bioinformatics.babraham.ac.uk/training.html#bsseq) material and have a look at slides...
Forum: Bioinformatics 06-10-2016, 03:36 AM
Replies: 313
Views: 91,495
Posted By simonandrews
The down-weighting here is simply the...

The down-weighting here is simply the proportional space offered to each of the tracks. The point being that for an annotation track with the same layout then once you have around 50px of vertical...
Forum: Bioinformatics 06-09-2016, 01:52 AM
Replies: 313
Views: 91,495
Posted By simonandrews
There's always a trade-off to make in these kinds...

There's always a trade-off to make in these kinds of display and internally we've tried a few different ways to adjust the layout to try to show more stuff on screen clearly but have kept with the...
Forum: Bioinformatics 05-17-2016, 07:50 AM
Replies: 313
Views: 91,495
Posted By simonandrews
Can you try deleting the cache folder in your...

Can you try deleting the cache folder in your assembly folder. SeqMonk might not have recognised that those files have changed and be using an older version.

If it's still not working for you...
Forum: Bioinformatics 05-12-2016, 04:26 AM
Replies: 313
Views: 91,495
Posted By simonandrews
There's no built in support for this kind of...

There's no built in support for this kind of customisation, but you could build this yourself if you like.

If you have a look in the automated genome you will quickly see how to play around with...
Forum: Bioinformatics 04-08-2016, 02:21 AM
Replies: 365
Views: 163,217
Posted By simonandrews
QCFail is our attempt to provide some kind of...

QCFail is our attempt to provide some kind of collation of the types of failures we see in sequencing experiements, not just stuff you could spot with FastQC, but all through the analysis pipeline. ...
Forum: Bioinformatics 04-01-2016, 06:51 AM
Replies: 1
Views: 1,135
Posted By simonandrews
If it's any consolation we gave up trying to...

If it's any consolation we gave up trying to understand all of the fastq-dump errors we saw and we now have a loop in our pipeline which simply tries the command again (up to 5 times) before deciding...
Forum: Illumina/Solexa 10-27-2015, 10:05 AM
Replies: 35
Views: 16,689
Posted By simonandrews
Whoever made the library should have a rough idea...

Whoever made the library should have a rough idea of the size selection they used when creating the library from which you can work out the insert size range. It will be an approximate range though,...
Forum: Illumina/Solexa 10-27-2015, 07:06 AM
Replies: 35
Views: 16,689
Posted By simonandrews
It depends on the insert size you have in your...

It depends on the insert size you have in your library. If a lot of your inserts are long enough that the overlap between your reads will be short or non-existent then you won't be able to merge...
Forum: Illumina/Solexa 10-22-2015, 05:08 AM
Replies: 8
Views: 8,497
Posted By simonandrews
Yes, Phred scores of 38 is plenty good enough -...

Yes, Phred scores of 38 is plenty good enough - however the problems you're likely to hit from FFPE material are not likely to result in poor sequencing scores, but in high duplication levels, or...
Forum: Bioinformatics 09-09-2015, 08:21 AM
Replies: 313
Views: 91,495
Posted By simonandrews
SeqMonk v0.32.1 has just been released. This...

SeqMonk v0.32.1 has just been released. This fixes a bug which meant that on some systems the dialog which showed the progress of R scripts could hang. We've also taken the opportunity to improve...
Forum: Bioinformatics 08-11-2015, 04:06 AM
Replies: 365
Views: 163,217
Posted By simonandrews
I've had a look at this and can kind of confirm...

I've had a look at this and can kind of confirm what you're seeing. Turning on the ignore flag for the per-tile module does now exclude that module from appearing in the report, however it wasn't...
Forum: Bioinformatics 07-30-2015, 06:47 AM
Replies: 365
Views: 163,217
Posted By simonandrews
That error suggests that one of the bundled jar...

That error suggests that one of the bundled jar files which ships with FastQC (jbzip2-0.9.jar) was missing from your installation.

Quickest and easiest fix would be to download the latest version,...
Forum: Bioinformatics 07-01-2015, 08:23 AM
Replies: 313
Views: 91,495
Posted By simonandrews
We've just released seqmonk v0.31.0 onto the...

We've just released seqmonk v0.31.0 onto the project web site. We've added some new options for analysing RNA-Seq and BS-Seq data and have tidied up the user interface for cases where you have long...
Forum: Bioinformatics 06-29-2015, 01:49 AM
Replies: 67
Views: 18,510
Posted By simonandrews
There isn't a publication for fastq_screen. We...

There isn't a publication for fastq_screen. We recommend just citing the project URL.
Forum: Bioinformatics 06-23-2015, 12:56 AM
Replies: 313
Views: 91,495
Posted By simonandrews
If you want the raw annotations which seqmonk...

If you want the raw annotations which seqmonk loads then you can just go to the Genomes folder where you'll find a set of .dat files which are EMBL format sequence header files which contain all of...
Forum: Bioinformatics 04-30-2015, 12:04 AM
Replies: 313
Views: 91,495
Posted By simonandrews
You can already make a track out of a subset of...

You can already make a track out of a subset of an existing track. In your case if you have a list of gene names then you could do:

Edit > Find named features

Paste your list of names into the...
Forum: Bioinformatics 04-27-2015, 03:02 AM
Replies: 313
Views: 91,495
Posted By simonandrews
Is this RNA-Seq or small RNA? What is the...

Is this RNA-Seq or small RNA? What is the quantitation? Did you do the corresponding QC plot for the data type you're using - if so, what did that look like? You said you did two levels of...
Forum: Bioinformatics 04-27-2015, 12:50 AM
Replies: 313
Views: 91,495
Posted By simonandrews
I can't see anything attached...

I can't see anything attached...
Forum: Bioinformatics 04-25-2015, 01:44 PM
Replies: 313
Views: 91,495
Posted By simonandrews
The RNA-Seq quantitation has been in for a while,...

The RNA-Seq quantitation has been in for a while, but we now make it easy to link out to DESeq and EdgeR without having to leave the program.

For smallRNAs you could still use the RNA-Seq pipeline...
Forum: Bioinformatics 04-23-2015, 07:14 AM
Replies: 313
Views: 91,495
Posted By simonandrews
I've just released seqmonk v0.30.0 on the project...

I've just released seqmonk v0.30.0 on the project web site (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/).

This version adds an optional link between seqmonk and a local R...
Forum: Bioinformatics 03-25-2015, 02:57 AM
Replies: 365
Views: 163,217
Posted By simonandrews
FastQC v0.11.3 has just been released. It fixes...

FastQC v0.11.3 has just been released. It fixes a few annoying bugs which have been mentioned on here before, and adds some support for processing folders of nanopore sequencing reads in HDF5...
Forum: Bioinformatics 03-02-2015, 12:27 PM
Replies: 15
Views: 4,197
Posted By simonandrews
Without seeing what options you used for the...

Without seeing what options you used for the quantitation it's difficult to know why you didn't get the value you expected.

Assuming you have a normal, unspliced library and that you really want...
Forum: Bioinformatics 03-02-2015, 08:35 AM
Replies: 15
Views: 4,197
Posted By simonandrews
Once you've done a quantitation you should just...

Once you've done a quantitation you should just be able to make up an annotated probe report (Reports > Annotated Probe Report) to make a report with the positions of the probes and the current...
Forum: Bioinformatics 02-24-2015, 01:15 AM
Replies: 365
Views: 163,217
Posted By simonandrews
All of the example reports shown on the fastqc...

All of the example reports shown on the fastqc project page also have the accompanying text output available (just not linked from the html page), so you're welcome to download those.
...
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