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Forum: RNA Sequencing 05-10-2017, 07:51 AM
Replies: 0
Views: 2,297
Posted By glados
edit: retracted

edit: retracted
Forum: Bioinformatics 04-22-2014, 04:42 AM
Replies: 1
Views: 1,720
Posted By glados
cummeRbund PCA plot

Can anyone explain cummeRbund's PCA plot?
I posted this question earleir in the RNA-sequencing forum but never got any replies so will try here in the Bioinformatics forum.

I do understand...
Forum: RNA Sequencing 04-15-2014, 02:08 PM
Replies: 0
Views: 1,967
Posted By glados
cummeRbund PCA plot

Can anyone explain cummeRbund's PCA plot?
I do understand traditional PCA plots, like the one in DESeq, and cummeRbund's MDS plot, but what does everything in cummeRbund's PCA version mean? What are...
Forum: RNA Sequencing 03-24-2014, 01:41 AM
Replies: 2
Views: 1,438
Posted By glados
Correlate expression levels with phenotypic measure?

Dear all.
I've been spending lots of time searching for an answer to this question, going through papers and discussing with people.

We have gene expression levels in 3 individuals that we want...
Forum: Bioinformatics 07-04-2013, 07:02 AM
Replies: 2
Views: 1,815
Posted By glados
I get the same problem. I get several gene_ids...

I get the same problem. I get several gene_ids with identical coordinates. It's so frustrating. How come cufflinks don't understand it is only one gene when they have identical coordinates? (using...
Forum: RNA Sequencing 07-01-2013, 08:00 AM
Replies: 5
Views: 3,582
Posted By glados
I also want to change the replicate names in...

I also want to change the replicate names in cummeRbund, since it gives them own replicate names with numbers from 0 and up. I've tried this:

replicates(cuff)$rep_name <-...
Forum: RNA Sequencing 07-01-2013, 07:51 AM
Replies: 5
Views: 3,582
Posted By glados
Same here. For the scatter plots and some other...

Same here. For the scatter plots and some other plots the code:
+ geom_point(aes(scale_size=2, scale_shape=19))
works great to add to the plot in order to change point size, etc.

But that does...
Forum: RNA Sequencing 06-25-2013, 06:21 AM
Replies: 35
Views: 25,766
Posted By glados
Same thing for me, getting A LOT of more...

Same thing for me, getting A LOT of more significantly different genes (tried with 2 different projects). Though I assumed that was intended.
Forum: Bioinformatics 06-04-2013, 01:02 PM
Replies: 9
Views: 5,159
Posted By glados
Roxana, I just tried out your perl script, and it...

Roxana, I just tried out your perl script, and it worked perfectly! (didn't have time earlier)
Thank you so much! Very useful! I will definitely have more use of your code. Thanks again!
Forum: Bioinformatics 05-28-2013, 01:52 PM
Replies: 9
Views: 5,159
Posted By glados
Yes, my coding skills are poor. Is it possible to...

Yes, my coding skills are poor. Is it possible to grep for any keyword related to homozygotic variants in the vcf-file?
Forum: Bioinformatics 05-28-2013, 01:23 PM
Replies: 9
Views: 5,159
Posted By glados
How do I do this? Any suggestion? I can't seem to...

How do I do this? Any suggestion? I can't seem to find a solution on how to do this.
Forum: Bioinformatics 05-03-2013, 01:28 PM
Replies: 5
Views: 2,221
Posted By glados
Wondering this as well.

Wondering this as well.
Forum: Bioinformatics 02-06-2013, 01:31 AM
Replies: 0
Views: 2,130
Posted By glados
Warning: Serious bug in Samtools depth

Samtools depth caps coverage values at around 8000.

I merged together a few bam-files to look at total coverage. I had a hard time understanding why all the different chromosomes had maximum...
Forum: Bioinformatics 01-22-2013, 04:34 AM
Replies: 313
Views: 111,566
Posted By glados
Dear Simon. I sent you a private message a...

Dear Simon.

I sent you a private message a few weeks ago. Perhaps you can take a look at it? It was a question regarding installing a custom genome.
Forum: Bioinformatics 12-12-2012, 02:58 AM
Replies: 5
Views: 2,351
Posted By glados
ekimmike, did you ever find out why you plot...

ekimmike, did you ever find out why you plot looked like that?
Forum: RNA Sequencing 12-12-2012, 02:53 AM
Replies: 37
Views: 19,860
Posted By glados
Dear figo1019. Make sure the lab meant 180...

Dear figo1019.

Make sure the lab meant 180 as insert size and not inner distance. If I were you, I would try with both the default and -8 as inner distance. See if you get any differences in...
Forum: Bioinformatics 12-04-2012, 02:49 AM
Replies: 9
Views: 2,469
Posted By glados
I'm wondering the same thing as vpp605. I am...

I'm wondering the same thing as vpp605.
I am separating the significant genes into up- and down-regulated as well, because I have two very different groups.
Forum: Bioinformatics 10-30-2012, 05:57 AM
Replies: 41
Views: 17,211
Posted By glados
Dear all. I'm trying to find information...

Dear all.

I'm trying to find information about how HTSeq counts reads. I understood that one pair (properly paired) is counted as 1 count.
What about pairs that are not flagged as 'properly...
Forum: Bioinformatics 10-10-2012, 02:04 AM
Replies: 5
Views: 2,351
Posted By glados
I have the same problem, though my plots look...

I have the same problem, though my plots look much more skewed than that. If it's not library construction, then what could it be? Can there be a biological reason? My groups are very different from...
Forum: Bioinformatics 09-13-2012, 08:51 AM
Replies: 4
Views: 1,421
Posted By glados
Thank you dariober for contributing with your...

Thank you dariober for contributing with your code! It works great!
Forum: Bioinformatics 09-12-2012, 02:55 AM
Replies: 4
Views: 1,421
Posted By glados
Yes, by using a reference annotation gtf. How do...

Yes, by using a reference annotation gtf. How do you suggest I use it? If I have a long list with genes I want to look at. Perhaps I can compare them somehow. I'm new to bioinformatics so it's not...
Forum: Bioinformatics 09-11-2012, 07:05 AM
Replies: 21
Views: 4,865
Posted By glados
I have had similar experience with Cuffdiff and...

I have had similar experience with Cuffdiff and have as well switched to DESeq as Bill Stevens did. Got completely different results compared to Cuffdiff which makes it pretty much impossible for me...
Forum: Bioinformatics 09-11-2012, 02:09 AM
Replies: 4
Views: 1,421
Posted By glados
DESeq - get chromosome

Hello all.

I've been searching for this question for hours now, and I give up and post it here instead. It should not be very complicated.

I have a long list of sig. genes in DESeq I would like...
Forum: RNA Sequencing 09-07-2012, 04:14 AM
Replies: 7
Views: 1,945
Posted By glados
You do not need to run cufflinks before cuffdiff!...

You do not need to run cufflinks before cuffdiff! Especially not if you're not interested in new genes/isoforms. Then just use your annotation gtf and the bam files. They even mention it in the...
Forum: Bioinformatics 08-28-2012, 02:29 AM
Replies: 3
Views: 1,608
Posted By glados
I had this problem as well. When I increased the...

I had this problem as well. When I increased the sample size, the number if sig. genes decreased drastically in cuffdiff. However I got the opposite result in DESeq, much more sig. genes with more...
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