User: Mthabisi Moyo

gravatar for Mthabisi Moyo
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2 years, 4 months ago
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m***************@u.northwestern.edu

Posts by Mthabisi Moyo

<prev • 10 results • page 1 of 1 • next >
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ntop parameter in plotPCA(). DESeq2
... Given that the PCA plot is likely to change somewhat depending on the number of genes you decide to specify with the ntop parameter, are there any recommendations on how to best set this value besides arbitrarily setting it at the default of 500/1000? Could including all genes have a negative effect ...
deseq2 written 6 days ago by Mthabisi Moyo10 • updated 4 days ago by Michael Love18k
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Blocking factors for differential binding analysis with DiffBind
... I have performed ChIP-seq for multiple transcription factors on samples from multiple patients. All ChIPs for each patient where sequenced on different sequencing runs (i.e. TF1, TF2, TF3 for patient 1 was on one flowcell and  TF1, TF2, TF3 for patient 2 was on a separate flowcell etc). I am looking ...
diffbind written 12 days ago by Mthabisi Moyo10
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Changing box plot font sizes for axes and labels in DiffBind
... I have been trying to change font sizes for my box plots in DiffBind: dba.plotBox(x, th = 0.05, pars = list(cex.axis=1.5, cex.main=2, cex.lab=1.5)) I have also tried the following variation: dba.plotBox(x, th = 0.05, cex.axis=1.5, cex.main=2, cex.lab=1.5) I assumed that these arguments would b ...
diffbind written 12 days ago by Mthabisi Moyo10
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Comment: C: ensDbFromGtf error from gtf file downloaded from GENCODE.
... I missed that, thanks for the catch! Deleting the .AnnotationHub folder cleared the cache and did the trick. I ran ensembldb using both the EnsDb I made from the Ensembl GRCh38 .gtf annotation file (v90) and the one I downloaded through AnnotationHub and both worked well. The only point I would mak ...
written 9 months ago by Mthabisi Moyo10
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Comment: C: ensDbFromGtf error from gtf file downloaded from GENCODE.
... I deleted the .AnnotationHub folder in /Library/Frameworks/R.framework/Versions/3.4/Resources/library/AnnotationHub and the result is unchanged. I still get 0 queries after reinstalling AnnotationHub database using Biocinstaller. Mthabisi   ...
written 9 months ago by Mthabisi Moyo10
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Comment: C: ensDbFromGtf error from gtf file downloaded from GENCODE.
... Thanks for the feedback! 1) I was able to construct the package using Ensembl 90 without a problem: >gtffile <- "/user/Downloads/Homo_sapiens.GRCh38.90.gtf.gz" > DB <- ensDbFromGtf(gtffile) Importing GTF file ... OK Processing metadata ... OK Processing genes ... Attribute availabi ...
written 9 months ago by Mthabisi Moyo10
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ensDbFromGtf error from gtf file downloaded from GENCODE.
... I am getting an error when I try and create an ensDb object using a GENCODE .gtf annotation file for GRCh38 downloaded directly from the GENCODE website. > gtffile <- "/user/Downloads/gencode.v26.annotation.gtf" > DB <- ensDbFromGtf(gtffile) Error in `colnames<-`(`*tmp*`, value = c ...
ensembldb ensdbfromgtf written 9 months ago by Mthabisi Moyo10 • updated 9 months ago by Johannes Rainer1.3k
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Comment: C: DEXSeq-Error in FUN(X[[i]], ...) : subscript out of bounds
... Hi Alejandro, It turns out it was likely the GENCODE gtf file. Switched to the mouse annotation file on Ensembl and it worked well. It is still odd to me considering the count files were created using the GENCODE gtf so I thought it would still result with the same number of lines but I guess not. ...
written 19 months ago by Mthabisi Moyo10
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DEXSeq-Error in FUN(X[[i]], ...) : subscript out of bounds
... I am trying to use DEXSeq to analyze a mouse paired-end stranded RNA-seq data (poly-A RNA capture). I Aligned the reads using STAR and obtained the reference genome and annotation file (which I collapsed with dexseq_prepare_annotation.py) from GENCODE (release m11). I used HTSeq to count exons (usin ...
dexseq written 19 months ago by Mthabisi Moyo10
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Comment: C: Getting Introns Expression at a Per Gene Level
... Hi Valerie, I am trying to do the same analysis as Fong i.e. count introns. I made a GRangesList of introns by gene as you described and also made a GRangesList of exons by gene using "exonsByGene <- exonsBy(txdb, by = c("gene"))." I wanted to test out counting using summarizeOverlaps and so I t ...
written 2.3 years ago by Mthabisi Moyo10

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