User: stianlagstad

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stianlagstad70
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Posts by stianlagstad

<prev • 61 results • page 1 of 7 • next >
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Gviz: Possible 5' and 3' marker errors
... This code: ``` transcriptID <- "ENST00000395443" mart <- biomaRt::useMart(   biomart = "ENSEMBL_MART_ENSEMBL",   dataset = "hsapiens_gene_ensembl",   host = "dec2013.archive.ensembl.org") # Create transcript track biomartTrack <- Gviz::BiomartGeneRegionTrack(   filters = list(     ensembl ...
software error written 27 days ago by stianlagstad70
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Comment: C: chimeraviz - import own fusion file for visualization
... No problem! Just ask more here or create an issue in the github repository if there's anything else. ...
written 4 months ago by stianlagstad70
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Answer: A: chimeraviz - import own fusion file for visualization
... Thank you for your interest in using chimeraviz!:) You can use your own file with the import functions like this: # Load chimeraviz library(chimeraviz) # A reference to your fusion file myfile <- "/home/stian/dev/soapfuse_833ke_final.Fusion.specific.for.genes" fusions <- importSoapfuse(myfil ...
written 4 months ago by stianlagstad70
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Comment: C: Gviz/Biostrings memory issue?
... Alright. Thanks again! ...
written 11 months ago by stianlagstad70
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Comment: C: Gviz/Biostrings memory issue?
... I was hoping something could be done about that, since I'm not interested in showing the reads. Could it not be possible to count the coverage without holding everything in memory? ...
written 11 months ago by stianlagstad70
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Comment: C: Gviz/Biostrings memory issue?
... Thank you for responding. I'm saying that when I run plotTracks like in my post, my R session stops responding because it is demanding too much memory. The only way out is to shut down the program (killall rstudio). Were you abel to produce the plot I tried to plot? ...
written 11 months ago by stianlagstad70
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Gviz/Biostrings memory issue?
... I'm running into memory issues trying to plot a region from a .BAM file produced from RACE-seq. The .BAM file is not huge, but the high coverage might be the problem. Here's an example: # Reproducing the memory problem # First, source this alternative bam-file import function for use with Gviz::Al ...
biostrings gviz written 11 months ago by stianlagstad70
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Comment: C: ensembldb: ensDbFromGtf error with ensembl version 74
... Thank you for the quick response. If I include "exon_idx" in the list given to columns, I don't end up getting a column in the metadata named "exon_idx". I do still get the "exon_rank" metadata column though, without asking for it. Should I create issues in the github repository if I find more bugs ...
written 18 months ago by stianlagstad70
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Comment: C: ensembldb: ensDbFromGtf error with ensembl version 74
... Hi again, I think I've stumbled across a little bug. When using exonsBy, even with "tx_id" in the list given to the columns parameter, I do not see a column in the metadata that says tx_id. Example: library(ensembldb) edb <- ensDbFromGtf(gtf = "/home/stian/Desktop/Homo_sapiens.GRCh37.74.gtf") ...
written 18 months ago by stianlagstad70
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Comment: C: Gviz: How to plot UTRs with GRanges object?
... I'm sorry about the confusion. What I want to accomplish is to build the structure I have to provide to Gviz manually, so that I produce the same plot as with BiomartGeneRegionTrack. That is, I wish to extract the relevant data from the TxDb myself, create a GRanges object with everything that is ne ...
written 18 months ago by stianlagstad70

Latest awards to stianlagstad

Supporter 19 months ago, voted at least 25 times.
Scholar 19 months ago, created an answer that has been accepted. For A: Gviz: Given transcript names and TxDb, how do you plot grouped transcripts?
Scholar 20 months ago, created an answer that has been accepted. For A: Gviz: Given transcript names and TxDb, how do you plot grouped transcripts?

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