Forum: Bioinformatics
04-21-2016, 06:05 AM
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Replies: 10
Views: 3,865
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!
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Forum: Bioinformatics
04-21-2016, 02:38 AM
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Replies: 10
Views: 3,865
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Forum: Bioinformatics
04-21-2016, 02:15 AM
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Replies: 10
Views: 3,865
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Forum: Bioinformatics
04-21-2016, 01:51 AM
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Replies: 10
Views: 3,865
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Forum: Bioinformatics
04-21-2016, 12:41 AM
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Replies: 10
Views: 3,865
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
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Forum: Bioinformatics
11-05-2015, 01:30 AM
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Replies: 10
Views: 3,865
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...
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Forum: Bioinformatics
09-11-2015, 09:17 AM
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Replies: 0
Views: 832
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...
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Forum: Bioinformatics
09-10-2015, 11:07 AM
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Replies: 3
Views: 3,633
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...
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Forum: Bioinformatics
09-07-2015, 06:38 AM
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Replies: 2
Views: 931
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...
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Forum: RNA Sequencing
09-03-2015, 09:48 AM
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Replies: 0
Views: 2,891
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...
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Forum: Bioinformatics
07-28-2015, 10:50 AM
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Replies: 1
Views: 702
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...
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Forum: Bioinformatics
07-24-2015, 06:40 AM
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Replies: 1
Views: 702
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,...
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Forum: Bioinformatics
07-24-2015, 05:45 AM
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Replies: 0
Views: 560
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...
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Forum: Introductions
07-24-2015, 04:35 AM
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Replies: 0
Views: 888
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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