Forum: Bioinformatics
07-05-2019, 04:00 AM
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Replies: 1
Views: 849
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Forum: Bioinformatics
09-10-2018, 02:25 AM
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Replies: 2
Views: 1,299
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...
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Forum: Bioinformatics
06-10-2016, 03:36 AM
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Replies: 313
Views: 110,368
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...
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Forum: Bioinformatics
06-09-2016, 01:52 AM
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Replies: 313
Views: 110,368
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Forum: Bioinformatics
05-17-2016, 07:50 AM
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Replies: 313
Views: 110,368
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...
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Forum: Bioinformatics
05-12-2016, 04:26 AM
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Replies: 313
Views: 110,368
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...
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Forum: Bioinformatics
04-08-2016, 02:21 AM
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Replies: 366
Views: 202,264
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. ...
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Forum: Bioinformatics
04-01-2016, 06:51 AM
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Replies: 1
Views: 1,734
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...
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Forum: Illumina/Solexa
10-27-2015, 10:05 AM
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Replies: 35
Views: 20,676
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Forum: Illumina/Solexa
10-27-2015, 07:06 AM
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Replies: 35
Views: 20,676
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...
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Forum: Illumina/Solexa
10-22-2015, 05:08 AM
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Replies: 8
Views: 9,349
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Forum: Bioinformatics
09-09-2015, 08:21 AM
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Replies: 313
Views: 110,368
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...
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Forum: Bioinformatics
08-11-2015, 04:06 AM
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Replies: 366
Views: 202,264
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Forum: Bioinformatics
07-30-2015, 06:47 AM
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Replies: 366
Views: 202,264
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,...
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Forum: Bioinformatics
07-01-2015, 08:23 AM
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Replies: 313
Views: 110,368
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...
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Forum: Bioinformatics
06-29-2015, 01:49 AM
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Replies: 67
Views: 25,008
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Forum: Bioinformatics
06-23-2015, 12:56 AM
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Replies: 313
Views: 110,368
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...
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Forum: Bioinformatics
04-30-2015, 12:04 AM
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Replies: 313
Views: 110,368
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Forum: Bioinformatics
04-27-2015, 03:02 AM
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Replies: 313
Views: 110,368
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...
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Forum: Bioinformatics
04-27-2015, 12:50 AM
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Replies: 313
Views: 110,368
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Forum: Bioinformatics
04-25-2015, 01:44 PM
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Replies: 313
Views: 110,368
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Forum: Bioinformatics
04-23-2015, 07:14 AM
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Replies: 313
Views: 110,368
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Forum: Bioinformatics
03-25-2015, 02:57 AM
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Replies: 366
Views: 202,264
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Forum: Bioinformatics
03-02-2015, 12:27 PM
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Replies: 15
Views: 5,198
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...
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Forum: Bioinformatics
03-02-2015, 08:35 AM
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Replies: 15
Views: 5,198
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