User: anupriyaverma1408

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Posts by anupriyaverma1408

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Plotting DataTrack for non-model organism.
... Hi all! Today I was trying the package called 'Gviz' for plotting chip-seq peaks as histogram across the whole genome of Mycobacterium tuberculosis. But I was unsuccessful as it keep giving this error:  Error in .normargGenome(value, seqnames(x)) :    supplied 'genome' must be a vector or factor ...
chipseq gviz plot written 18 months ago by anupriyaverma14080
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Chip-seq peak annotation [Chipseeker]
... Hi all,  I was dealing with this package called 'Chipseeker' . I tried annotating a chip-seq peak calls fro Mycobacterium tuberculosis. As there is no 'org.Mtu.eg.db' package for annotation &  'TxDB' can be used in Chipseeker,  so I created TxDB package & annotated as follows : library(Gen ...
annotation chipseeker chip-seq guangchuang written 21 months ago by anupriyaverma14080 • updated 21 months ago by Guangchuang Yu1.1k
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Comment: C: CNV parameter not working - MEDIPS
... Hi Matthias, I've one more doubt. After getting annotations with MEDIPS.getAnnotation function I'm getting some annotations that are having only Ensembl enzyme/protein/transcript ID (no geneIDs)  : chr    start    stop    chr.1    start.1    stop.1    CF    X1.WT.5mC_S1.bam.counts    X2.LshKO.5mC_ ...
written 22 months ago by anupriyaverma14080
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Comment: C: CNV parameter not working - MEDIPS
... Hi Matthias, Thanks a lot. It worked the way you told me. Sub-setting the chromosome set using -> chr.select=paste0("chr",c(1:19,"X",Y")) was the thing that was needed. Now MEDIPS.meth is also working with 'CNV = T'.  Can MEDIPS be used to get CNVs for one MSet say MSet1 ? : mr.edgeR_LshKO = ME ...
written 22 months ago by anupriyaverma14080
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CNV parameter not working - MEDIPS
... I ran following sets of commands for getting differential methylation profiles & CNVs : library(MEDIPS) library(BSgenome.Mmusculus.UCSC.mm9) BSgenome="BSgenome.Mmusculus.UCSC.mm9" uniq=1e-3 extend=300 shift=0 ws=100 WT_Input = MEDIPS.createSet(file = "/Medip-seq_project/Alignment_BAMs_an ...
medips error medip-seq lukas written 22 months ago by anupriyaverma14080 • updated 22 months ago by Matthias Lienhard140
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Window size for MEDIPS
... Hello all, I've been trying a package called 'MEDIPS' for MeDIP-seq analysis for few days now. The manual says : The genome will be divided into adjacent windows of length 100nt and all further calculations (short read coverage, differential coverage between conditions etc.) will be applied to these ...
medips peak finding medip-seq luckas written 22 months ago by anupriyaverma14080 • updated 22 months ago by Lukas Chavez510

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