User: hirahameed222

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Posts by hirahameed222

<prev • 21 results • page 1 of 3 • next >
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How to perfrom Gene Ontology for ID's starting wih "TraesCS"
... Hi there. I used HISAT2 for the alingment, Stringtie for the assembly and the R package Ballgown for the Differential Expression (DE) analysis (protocol published here: http://www.nature.com/nprot/journal/v11/n9/full/nprot.2016.095.html ). Now, i want to do gene ontology by using AGRIGO which only a ...
genome R next-gen rna-seq gene written 3 months ago by hirahameed2220
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Comment: C: how to display gene names rather than MSTRG (using ballgown)
... It's really helpful. Thanks ! ...
written 4 months ago by hirahameed2220
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how to display gene names rather than MSTRG (using ballgown)
... Hi there. I used HISAT2 for the alingment, Stringtie for the assembly and the R package Ballgown for the Differential Expression (DE) analysis (protocol published here: http://www.nature.com/nprot/journal/v11/n9/full/nprot.2016.095.html ). I used following commands. data_directory = system ...
software error R next-gen alignment written 4 months ago by hirahameed2220
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how to make an input file for DAVID Bioinformatics Tool for wheat's RNA seq data?
... Hi I am working on wheat RNA seq Data obtained via High Throughput Sequencing , as i am new to this work i am confused for input file required for DAVID > https://david-d.ncifcrf.gov/conversion.jsp?VFROM=NA. The nature protocol states about input file as:- > A list of gene identifiers is th ...
rna-seq written 4 months ago by hirahameed2220 • updated 4 months ago by jared.andrews072.8k
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Comment: C: Guildeline Required For Gene Ontology, after Differntial expression analysis
... can you please explain for wheat RNA-seq data Can i use this ? ...
written 4 months ago by hirahameed2220
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Comment: C: Guildeline Required For Gene Ontology, after Differntial expression analysis
... Can you please share any tutorial or guide me how to do this for basic Ontology process. I am new to deal with RNA-seq data and i am doing this work for the first time and it will be easy to learn if i follow some protocol. ...
written 4 months ago by hirahameed2220
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Guildeline Required For Gene Ontology, after Differntial expression analysis
... Hello! I have done differential expression analysis for my RNA-seq data set by following the HISAT, Stringtie and Ballgown protocol. The next thing i want to do is some basic gene ontology. Can anyone please suggest me some Tools, protocol to follow for desired work. Have you any guidelines ? Th ...
gene R next-gen rna-seq written 4 months ago by hirahameed2220 • updated 4 months ago by jared.andrews072.8k
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Comment: C: How to find gene names for csv files created by R
... feature id fc pval qval 1 gene ENSRNA050018849 1.4057356 0.5001672 0.5001672 2 gene ENSRNA050021620 0.8327369 0.5001672 0.5001672 3 gene MSTRG.1 0.7915044 0.5001672 0.5001672 ...
written 4 months ago by hirahameed2220 • updated 4 months ago by genomax70k
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(Closed) How to print tables for a particular command inR
... I am following this protocol for differential gene expression > https://kimlaborg.files.wordpress.com/2017/10/nprot-2016-095.pdf In order to identify transcripts and genes with a q value <0.05 the following command in used `subset(results_transcripts,results_transcripts$qval<0.05)>su ...
R written 4 months ago by hirahameed2220
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Comment: C: How to find gene names for csv files created by R
... yes, I followed the protocol exactly. ...
written 4 months ago by hirahameed2220

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