User: kaur.alasoo

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kaur.alasoo10
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Location:
University of Tartu, Tartu, Estonia
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http://kauralasoo.net/
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kauralasoo
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3 months ago
Joined:
1 year, 8 months ago
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Posts by kaur.alasoo

<prev • 5 results • page 1 of 1 • next >
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Comment: C: GenomicFeatures::makeTxDbFromEnsembl fails to create a TxDb object
... Thanks! That's very helpful! I wasn't aware that you could get the latest Ensembl annotations from AnnotationHub(). I knew about the EnsDb.Hsapiens.v86 package, but that's quite outdated by now.  ...
written 3 months ago by kaur.alasoo10
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GenomicFeatures::makeTxDbFromEnsembl fails to create a TxDb object
... I tried to create a TxDd object using the makeTxDbFromEnsembl function, but got the following error: txdb = GenomicFeatures::makeTxDbFromEnsembl(organism = "Homo sapiens") Fetch transcripts and genes from Ensembl ... OK Fetch exons and CDS from Ensembl ... OK Fetch chromosome names and lengths fro ...
genomicfeatures written 3 months ago by kaur.alasoo10 • updated 3 months ago by James W. MacDonald47k
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Answer: A: Plotting bigwig coverage over chromosomal coordinates with wiggleplotr
... Dear Michael, Thank you for the question. Yes, although it is not explicitly described in the vignette, wiggleplotr can be used to display ATAC-seq read coverage in a genomic region. For an example, see Figure 3D or Figure 4C in this paper :https://www.biorxiv.org/content/early/2017/05/18/102392. I ...
written 11 months ago by kaur.alasoo10
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Comment: C: GenomicFeatures makeTxDbFromBiomart fails with "unkown species" error
... Yes, you are right. Seems to be working now. Thanks! ...
written 19 months ago by kaur.alasoo10
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GenomicFeatures makeTxDbFromBiomart fails with "unkown species" error
... I tried to construct TxDb object from the latest version of Ensembl (v87): txdb87 = makeTxDbFromBiomart( biomart = "ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl", host="dec2016.archive.ensembl.org") But I got the following error: Download and preprocess the 'transcripts' data frame ...
biomart genomicfeatures maketxdbfrombiomart written 19 months ago by kaur.alasoo10 • updated 19 months ago by James W. MacDonald47k

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