User: Mthabisi Moyo

gravatar for Mthabisi Moyo
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1 month ago
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1 year, 9 months ago
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m***************@u.northwestern.edu

Posts by Mthabisi Moyo

<prev • 7 results • page 1 of 1 • next >
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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 weeks 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 10 weeks 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 10 weeks 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 10 weeks ago by Mthabisi Moyo10 • updated 10 weeks ago by Johannes Rainer1.1k
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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 12 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 12 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 20 months ago by Mthabisi Moyo10

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