User: Peng, Tao

gravatar for Peng, Tao
Peng, Tao170
Reputation:
170
Status:
New User
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Last seen:
6 years, 7 months ago
Joined:
6 years, 9 months ago
Email:
t****@fhcrc.org

Posts by Peng, Tao

<prev • 17 results • page 1 of 2 • next >
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Answer: A: Run Tophat In Galaxy
... Hi I wonder how I can quantitatively visualize expression of a gene/transcript which has a significant p-value/q value from splicing differential testing from Cuffdiff analysis? I tried track browser in GALAXY and UCSC genome browser and none of them really provide a quantitative analysis of gene/tr ...
written 6.6 years ago by Peng, Tao170
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Comment: C: Run Tophat In Galaxy
... Thanks a lot. Please see the attached screen shot from using Browser in GALAXY for viewing results of Tophat. What do those numbers mean? Is there any way to adjust Y-axis to have the bar taller so it will be easier to see? Thanks, tao To: Peng, Tao Cc: galaxy-user Subject: Re: [galaxy-user] run ...
written 6.6 years ago by Peng, Tao170
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Comment: C: Run Tophat In Galaxy
... Jen, thank you for following up on my question. Is any tool in GALAXY to visualize the coverage of aligned reads from TopHat on human chromosomes (histogram or density plot)? Tao To: galaxy-user Cc: Peng, Tao Subject: Re: [galaxy-user] run tophat in galaxy ===> Please use "Reply All" when resp ...
written 6.7 years ago by Peng, Tao170
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Comment: C: Run Tophat In Galaxy
... Hi when I am done with cuffdiff analysis in GALAXY, I got many tabular data output for gene, transcript, promoter and CDS differential expression testing, I wonder if there are some systematic ways to look at the data output from cuffdiff analysis? Thanks, tao ...
written 6.7 years ago by Peng, Tao170
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Answer: A: Running Cufflinks
... Hi I had 3 GTF files from ensemble, UCSC and NCBI for annotation; ONLY ensemble were recognized by GALAXY cufflinks as a GTF file although they all have .GTF. I am NOT sure why UCSC and NCBI GTF files were seen as GFF files? Thx, tao To: galaxy-user Cc: Peng, Tao Subject: running cufflinks == ...
written 6.7 years ago by Peng, Tao170
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Running Cufflinks
... Hi I am NOT sure why running cufflinks failed here. Thanks for your suggestion, tao Tool: Cufflinks Name: Cufflinks on data 6 and data 26: assembled transcripts Created: Sep 01, 2011 Filesize: 81.3 Mb Dbkey: hg19 Format: gtf Tool Version: Input Parameter Value SAM or BAM f ...
cufflinks rna-seq written 6.7 years ago by Peng, Tao170
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Answer: A: Annotation File For Cufflinks
... Hi I have down-loaded UCSC HG19 annotation files from Cufflinks; Should I just load genes.GTF file (about 100 MB) to galaxy for cufflink analysis? Thanks, tao To: Jennifer Jackson; galaxy-user; Peng, Tao Subject: Re: [galaxy-user] annotation file for cufflinks If using Ensembl make sure it is ...
written 6.7 years ago by Peng, Tao170
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Comment: C: Annotation File For Cufflinks
... In the cufflink site, they have annotation from ucsc,ncbi & ensemble. not sure which one to download and then load into galaxy? thanks, Tao Sent from my iPhone ...
written 6.7 years ago by Peng, Tao170
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Annotation File For Cufflinks
... Hi jen and galaxy users, when I try to use cufflinks in GALAXY and select "use reference annotation", I am NOT sure how to get the annotation file in GTF format for cufflinks. I was trying to down-load the annotation file from Illumina donated package in Cufflink website, I am NOT sure this is the ...
cufflinks rna-seq written 6.7 years ago by Peng, Tao170 • updated 6.7 years ago by Gary Xie10
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Run Tophat In Galaxy
... Hi how can I specify a GTF gene annotation file when running tophat to guide the alignment to human genome? What is the best way to visualize the tophat results in the context of annotated human genome, i.e. RefSeq? Thanks, tao ...
tophat rna-seq written 6.7 years ago by Peng, Tao170

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