User: harris

gravatar for harris
harris0
Reputation:
0
Status:
New User
Last seen:
5 months ago
Joined:
9 months, 2 weeks ago
Email:
h*****@uthscsa.edu

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by harris

<prev • 6 results • page 1 of 1 • next >
0
votes
1
answer
211
views
1
answer
converting mstrg labels from stringtie and prepDE.py to gene symbol for downstream biology
... Hi I have output from stringtie and making count files with prepDE.py. I then analyze with DESeq2 and have a list of DE genes. I have in this file both ensemble id and mstrg names for the genes and transcript files. I want to convert those mstrg and ensemble names to gene symbols for downstream anal ...
deseq2 written 5 months ago by harris0 • updated 5 months ago by Michael Love23k
0
votes
1
answer
210
views
1
answer
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 5 months ago by harris0 • updated 5 months ago by James W. MacDonald49k
0
votes
0
answers
214
views
0
answers
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 6 months ago by harris0 • updated 6 months ago by Michael Love23k
0
votes
2
answers
1.9k
views
2
answers
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 9 months ago by harris0
0
votes
6
answers
3.3k
views
6
answers
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 9 months ago by harris0
0
votes
0
answers
205
views
0
answers
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 9 months ago by harris0

Latest awards to harris

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 214 users visited in the last hour