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Forum: Bioinformatics 04-21-2016, 06:05 AM
Replies: 10
Views: 3,865
Posted By abisko00
Solved

Normally, I hate these kind of solutions, because you learn nothing from them, but after you've shown that the code is working, I did a clean install of R and Gviz and here we go!

Thanks!
Forum: Bioinformatics 04-21-2016, 02:38 AM
Replies: 10
Views: 3,865
Posted By abisko00
How did you produce your image? I am relatively...

How did you produce your image? I am relatively new to R and completely autodidactic. Maybe I miss a very simple setting. But thanks anyway!
Forum: Bioinformatics 04-21-2016, 02:15 AM
Replies: 10
Views: 3,865
Posted By abisko00
I attached what it produces on my system. I saved...

I attached what it produces on my system. I saved it as pdf, though, because that format is easiest to use in Illustrator.

pdf('test.pdf')
plotTracks(
c(gTrack, alTrack, alTrack2),
from =...
Forum: Bioinformatics 04-21-2016, 01:51 AM
Replies: 10
Views: 3,865
Posted By abisko00
You could also use the gapped.bam from the Gviz...

You could also use the gapped.bam from the Gviz sample data twice:

Setting the min.height parameter did not change it, unfortunately.
Forum: Bioinformatics 04-21-2016, 12:41 AM
Replies: 10
Views: 3,865
Posted By abisko00
Hi, thanks for pointing me to your thread....

Hi,

thanks for pointing me to your thread. Meanwhile, I have given up on this problem, but although my plot is slightly different, I'll give the max.height parameter a try.

Markus
Forum: Bioinformatics 11-05-2015, 01:30 AM
Replies: 10
Views: 3,865
Posted By abisko00
Gviz - adjust track height

Dear all,

I have a probably trivial problem where I need a hint into the right direction:

I am trying to visualize RNA-seq data in Gviz (nice!). I have two bam files loaded as AlignmentsTrack...
Forum: Bioinformatics 09-11-2015, 09:17 AM
Replies: 0
Views: 832
Posted By abisko00
Cufflinks: map transcripts_id to nearest_ref

I believe this is a very simple question, but since I am a scripting noob, I am completely lost:

In the merged.gtf (cuffmerge output), each transcript is assigned a TCONS_##### number. I have a...
Forum: Bioinformatics 09-10-2015, 11:07 AM
Replies: 3
Views: 3,633
Posted By abisko00
Hi! I would like to revive this thread, as I...

Hi!

I would like to revive this thread, as I am very much interested in an answer. Most alignment programs require this parameter and they all use different default settings. I would assume that...
Forum: Bioinformatics 09-07-2015, 06:38 AM
Replies: 2
Views: 931
Posted By abisko00
Hi Saeideh, I am new to Cufflinks myself,...

Hi Saeideh,

I am new to Cufflinks myself, but when you look at the tracking file, the gene_id should be listed here as well (column D?). It certainly depends on which reference annotation file...
Forum: RNA Sequencing 09-03-2015, 09:48 AM
Replies: 0
Views: 2,891
Posted By abisko00
Cufflinks and hg38 annotation

Dear all,

I would like to run cufflinks with reads aligned to the human GRCh38/hg38 genome assembly (download from UCSC). Cufflinks requires an annotation file with tss_id and p_id to allow...
Forum: Bioinformatics 07-28-2015, 10:50 AM
Replies: 1
Views: 702
Posted By abisko00
Short update to this question: the Tophat2...

Short update to this question:

the Tophat2 manual demands that the gtf-file uses the same chromosome identifiers as the bowtie-index.

This is clearly not the case, since as I said, the...
Forum: Bioinformatics 07-24-2015, 06:40 AM
Replies: 1
Views: 702
Posted By abisko00
hg19 genome and unassigned sequences

Hi!

I started working with RNA-seq data on an in-house Galaxy installation, but they did not have tophat installed, which I wanted to give a try. So I installed tophat2 on my own computer,...
Forum: Bioinformatics 07-24-2015, 05:45 AM
Replies: 0
Views: 560
Posted By abisko00
Read number confusion in tophat2

Dear all,

I am very new to RNA-seq and have plenty of questions. Please be patient if my questions are too stupid. Here's my first one:

When I run tophat2 (2.0.13) on my paired-end Illumina...
Forum: Introductions 07-24-2015, 04:35 AM
Replies: 0
Views: 888
Posted By abisko00
Greetings!

Dear all,

I am a biologist working closely with chemists in DNA/RNA modification research. Currently trying to make sense of my first RNAseq dataset.

Cheers,
abisko00
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