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Search: Posts Made By: sindrle
Forum: Bioinformatics 03-13-2017, 12:12 PM
Replies: 8
Views: 1,033
Posted By sindrle
Thats great! Any input on how to normalise...

Thats great!

Any input on how to normalise the counts? i.e. "counts/library size"?
Forum: Bioinformatics 03-13-2017, 11:55 AM
Replies: 8
Views: 1,033
Posted By sindrle
Thank you very much! The two transcripts...

Thank you very much!

The two transcripts each have 2 unique sections (exon-a1 for one, and exon-1b for the other). I guess I can just define where these sequences are, in a GTF-file?, and use...
Forum: Bioinformatics 03-13-2017, 08:03 AM
Replies: 8
Views: 1,033
Posted By sindrle
Ok, so I got the transcript-sequences for the two...

Ok, so I got the transcript-sequences for the two transcripts of interest. Can you please explain how I should use them as reference for Bowtie2 (file format etc.)? An example with code would be very...
Forum: Bioinformatics 03-12-2017, 05:57 AM
Replies: 8
Views: 1,033
Posted By sindrle
Thats interesting! Yes, I have the full...

Thats interesting!

Yes, I have the full transcript sequences. What do you think is the pros and cons between these approaches?
Forum: Bioinformatics 03-11-2017, 06:36 AM
Replies: 8
Views: 1,033
Posted By sindrle
Analysing only exons from ONE gene using RNAseq

I know that DEXseq and/or Cuffdiff etc. may be used of exon-levels analyses.

However, I am only interested in ONE gene, because a novel exon is discovered in this gene, by other researches. There...
Forum: RNA Sequencing 09-21-2014, 02:55 AM
Replies: 0
Views: 752
Posted By sindrle
Isoform quantification, sanity check

Hi!

Im studying adipose and skeletal muscle tissue atm. As a quick sanity check of Cuffdiff results on isoforms, I want to look at well described isoforms.

What I mean is to look at i.e. two...
Forum: Bioinformatics 09-05-2014, 04:21 AM
Replies: 5
Views: 1,582
Posted By sindrle
Yes, I agree.. Lots of errors on Osx.. ...

Yes, I agree.. Lots of errors on Osx..

Tuxedo-suite 2.1.1 works like a charm!


NB!
Wrong title, I meant 2.2.1!!! How can I update the title..
Forum: Bioinformatics 09-05-2014, 12:27 AM
Replies: 5
Views: 1,582
Posted By sindrle
Oh, sorry! Often many people have the same...

Oh, sorry! Often many people have the same problem and find a way to fix it, but maybe not for this errors..
Forum: Bioinformatics 09-04-2014, 03:07 PM
Replies: 5
Views: 1,582
Posted By sindrle
Compiling Cufflinks 2.1.1: Fatal error

Getting tired of "segmentation 11" errors I started compiling Cufflinks on osx maverick.

Im using Boost version 1.47 and everything works until the final steps:
...
Forum: Bioinformatics 08-30-2014, 06:29 PM
Replies: 0
Views: 726
Posted By sindrle
MixOmics

Hi!
I came across this package:

http://www.inside-r.org/packages/cran/mixOmics/docs/cim

Im running the cim() function after sPLS:

resultsPLS <- spls(X, Y, ncomp = 5, mode = "canonical",...
Forum: RNA Sequencing 08-18-2014, 06:29 AM
Replies: 1
Views: 1,068
Posted By sindrle
New transcript?

Hi!
We have measured a protein, but we get a much larger protein than the transcript should imply.

Using RNA-seq I assembled some transcript using Cufflinks->Cuffmerge to look for a new...
Forum: Bioinformatics 08-02-2014, 07:24 AM
Replies: 5
Views: 1,052
Posted By sindrle
Ok, thank you, Ill try that.

Ok, thank you, Ill try that.
Forum: Bioinformatics 08-02-2014, 03:52 AM
Replies: 5
Views: 1,052
Posted By sindrle
For simplicity, say you measured 5 gener using...

For simplicity, say you measured 5 gener using RT-PCR, and you measured 8 lipid species. All within the same tissue and at the same 6 time points. And you have 26 observations in each time point for...
Forum: Bioinformatics 08-02-2014, 03:08 AM
Replies: 5
Views: 1,052
Posted By sindrle
Human. Insulin pathway and lipid metabolism are...

Human. Insulin pathway and lipid metabolism are of great interest!
Forum: Bioinformatics 08-01-2014, 04:36 PM
Replies: 5
Views: 1,052
Posted By sindrle
Gene expression and lipids, time-series analysis

Hi!
I have two data sets; genes and lipids (RNAseq and lipidomics).
I have 6 time points (equal for both data sets).

How can I see how these two data sets influence each other? Should I use...
Forum: Bioinformatics 07-17-2014, 12:44 PM
Replies: 4
Views: 892
Posted By sindrle
Ok, thank you. Unfortunatly I have little...

Ok, thank you. Unfortunatly I have little experience with Micro Array, but I guess Ill manage.
Forum: Bioinformatics 07-17-2014, 12:20 PM
Replies: 4
Views: 892
Posted By sindrle
Lets say you want to search for highly expressed...

Lets say you want to search for highly expressed genes in a tissue that also is secreted, then its more likely you will find it i say blood plasma, since other tissues don't influence that much.
...
Forum: Bioinformatics 07-11-2014, 12:16 PM
Replies: 4
Views: 892
Posted By sindrle
BioGPS, command line?

Hi!
Just a question, I have seen some people using BioGPS to get a feel of where a certain gene is more/less expressed, in terms of tissues.

BioGPS only takes 10 inputs at a time and is a "point...
Forum: Bioinformatics 07-07-2014, 01:52 PM
Replies: 218
Views: 116,920
Posted By sindrle
Holy moly.

Holy moly.
Forum: Bioinformatics 07-07-2014, 01:35 PM
Replies: 218
Views: 116,920
Posted By sindrle
Quick question, on a fastq file Tophat2 spends...

Quick question, on a fastq file Tophat2 spends about 3-4h, STAR runs in 5 min - 1.5h.

How come only 5 min? Thats almost unbelievable.. It says success, but Im very sceptical..
Forum: RNA Sequencing 06-08-2014, 11:31 AM
Replies: 0
Views: 638
Posted By sindrle
How to analysing isoform thats not yet annotated

Hi!
I read a paper recently about PPARGC1A. I now want to look at how this isoform is regulated in a RNA seq set I have from human. This is the article, they analyse mouse, but found the ortholog in...
Forum: RNA Sequencing 05-27-2014, 07:40 AM
Replies: 14
Views: 5,785
Posted By sindrle
Haha! Yes, I was trying to sort everything...

Haha!
Yes, I was trying to sort everything nicely, since Im going to try a lot of things later. But of course I made a stupid mistake.

It works now, re-doing the analysis with one time point:
...
Forum: RNA Sequencing 05-27-2014, 06:50 AM
Replies: 14
Views: 5,785
Posted By sindrle
Thank you very much for all your help. For many...

Thank you very much for all your help. For many reasons I started over using FeatureCount.
But when I try to run DESeq2 now, I get an error:

DESeq2 error: inv(): matrix appears to be singular
...
Forum: Bioinformatics 05-26-2014, 01:03 AM
Replies: 149
Views: 48,000
Posted By sindrle
Im actually struggling with the following, I want...

Im actually struggling with the following, I want to easily create a DESeqDataSet from FeatureCounts. My goal is to use the
fpkm() function within DESeq2, not the one in FC.

In the DESeq2 help...
Forum: RNA Sequencing 05-26-2014, 12:36 AM
Replies: 14
Views: 5,785
Posted By sindrle
Thank you very much, most helpful. Checking...

Thank you very much, most helpful.

Checking the test with 1 time point gave exactly what you said, but I did not check p-values of the correlations.

When testing with two time points I got only...
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