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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Last seen:
6 months ago
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1 year, 3 months ago
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Posts by kaur.alasoo

<prev • 3 results • page 1 of 1 • next >
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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 6 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 14 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 14 months ago by kaur.alasoo10 • updated 14 months ago by James W. MacDonald46k

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