User: harris

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harris0
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Posts by harris

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coverting mstrg gene_id to gene symbols
... after running stringtie and making count matrix with prepDE.py  I need to covert the MSTRG.* gene_id to gene symbols. How do you do that . steve ...
bioconductor written 13 days ago by harris0 • updated 13 days ago by James W. MacDonald48k
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Getting gene symbols with ensemble ids and mstrg ids
... Hi DESeq fans and Michael love who designed. Learning pretty fast and getting output files. But need to put in the files, the gene symbol and have tried the  library(biomaRt) approach  , runs but does not put  GS into my data. Seems biomart can handle the ensemble ids if functional (seems maybe link ...
annotation written 25 days ago by harris0 • updated 25 days ago by Michael Love20k
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Comment: C: DESeq2 vs Ballgown results
...   hi ag1805x, have hisat2 and stringtie working, trying Ballgown, and having issue with  getting DE expression as I have for years, with cuffdiff. Now exploring other ways, and looks like DEseq2 is the best way to go or go back to cuffdiff.  For now I would like to try your suggestion. What is Feat ...
written 3 months ago by harris0
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Comment: C: StringTie + Ballgown: handling biological replicates
... hi Alyssa, new to R and ballgown. Have 16 samples run thru hisat2 with the --dta  and stringtie with -B option, made pheno_data, and ballgown dir with the 16 sample dir with the .ctab and .gtf  files  for each sample. Got to run in ballgown ok, and made .csv files for genes and transcripts.   What I ...
written 3 months ago by harris0
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Error loading data, pheno_data names in 1st column do not match ballgown/sample dir names.
... > library(ballgown) Attaching package: ‘ballgown’ The following object is masked from ‘package:base’:     structure > pheno_data=read.csv("C:/pheno_data/PSC3_phenodata.csv") > bg_PSC=ballgown(dataDir=("C:/ballgown"),samplePattern="PSC", pData=pheno_data) Sun Jul 08 17:56:17 2018 Sun Jul ...
ballgown written 4 months ago by harris0

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