User: Lucy

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Lucy0
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Posts by Lucy

<prev • 11 results • page 1 of 2 • next >
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Comment: C: bioMart error - The query to the BioMart webservice returned an invalid result:
... Great, thank you. This worked well. ...
written 6 weeks ago by Lucy0
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bioMart error - The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1
... Hi, Recently I have been getting an error with biomaRt that I didn't use to get with the same command. The error is: > Batch submitting query [============================================================>---] 95% eta: 29sError in getBM(attributes = c("ensembl_gene_id", "entrezgene", "hgnc_ ...
biomart written 6 weeks ago by Lucy0 • updated 6 weeks ago by Mike Smith3.8k
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Comment: C: sva::ComBat without covariate of interest?
... Hi, What is the current conclusion to this question? The manual I have (compiled May 22nd 2019) says to include covariate of interest, but then it doesn't seem to be included in the example? Many thanks, Lucy ...
written 11 weeks ago by Lucy0
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Comment: C: ChIPpeakAnno, MACS format annotation
... Sorry that isn't very easy to read! I would be happy to send you the file if it is easier. ...
written 7 months ago by Lucy0
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Comment: C: ChIPpeakAnno, MACS format annotation
... #!genome-build GRCh38.p12 #!genome-version GRCh38 #!genome-date 2013-12 #!genome-build-accession NCBI:GCA_000001405.27 #!genebuild-last-updated 2018-07 chr1 havana gene 11869 14409 . + . gene_id "ENSG00000223972"; gene_version "5"; gene_name "DDX11L1"; gene_source "havana"; g ...
written 7 months ago by Lucy0
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Comment: C: ChIPpeakAnno, MACS format annotation
... Thank you Julie. I wasn't sure whether I could use the GFF option as Ensembl states that "The GTF (General Transfer Format) is identical to GFF version 2" https://www.ensembl.org/info/website/upload/gff.html I have a matched RNA-seq dataset for which I used the Ensembl GTF file for annotation, so ...
written 7 months ago by Lucy0
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Comment: C: ChIPpeakAnno, MACS format annotation
... Hi, I am trying to make a custom annotation file to use with ChIPpeakAnno. I am starting with an Ensembl GTF file. The following command gives the error: **duplicated or NA names found. Rename all the names by numbers.** `annoData <- toGRanges(gff, format="GFF")` Which part of the GTF file d ...
written 7 months ago by Lucy0
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Best csaw normalization approach for ATAC-seq data
... Hi, I would like to use csaw to calculate effective library sizes for my ATAC-seq data so that I can then use these to generate normalized BigWig files. Would you recommend normalizing for composition biases or efficiency biases? I am struggling to decide which is most relevant for ATAC-seq. Many ...
csaw written 11 months ago by Lucy0 • updated 11 months ago by Aaron Lun24k
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Comment: C: EdgeR normalization factors - do they take into account library size?
... Great thank you. Yes, I am dealing with RNA-seq data, although I also have ATAC-seq data.  What would you recommend for scaling this? ...
written 11 months ago by Lucy0
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Comment: C: EdgeR normalization factors - do they take into account library size?
... Thank you Aaron and James.  I am actually trying to decide what to normalize by when I generate BigWig files using deepTools - should I use the edgeR normalization factor or the effective library size (normalization factor x library size) - the latter seems to make most sense? ...
written 11 months ago by Lucy0

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