User: Fang,Xiefan

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Fang,Xiefan30
Reputation:
30
Status:
New User
Location:
United States
Last seen:
1 year, 6 months ago
Joined:
5 years, 1 month ago
Email:
x*********@ufl.edu

Posts by Fang,Xiefan

<prev • 7 results • page 1 of 1 • next >
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Comment: C: Cufflinks: reference annotation file for Nile Tilapia (Oreochromis_niloticus)
... Thanks Jen. It turns out that the UCSC genome is OreNil2.0 and the ensembl annotation is OreNil1.0. I downloaded the ensembl tilapia genome (OreNil1.0) and did the tophat alignment again. This time, I could run cufflinks and HTseq with the ensembl annotation. ...
written 18 months ago by Fang,Xiefan30
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Cufflinks: reference annotation file for Nile Tilapia (Oreochromis_niloticus)
... I want to do differential gene expression analysis on some Nile Tilapia RNA-Seq data using the Cufflinks-Cuffdiff method. I aligned the sequence reads to the UCSC Nile Tilapia genome with >80% mapping efficiency. I downloaded the annotation GTF file from Ensembl and converted it using the "Make e ...
nile tilapia cufflinks annotation rna-seq written 19 months ago by Fang,Xiefan30
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Please add the zebrafish genome to tophat
... Can you add the latest zebrafish genome danio_rerio_zv10 to the tophat reference genome? Thank you very much! ...
genomes galaxy tophat written 2.3 years ago by Fang,Xiefan30 • updated 2.3 years ago by Jennifer Hillman Jackson23k
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Cuffdiff gene ID
... I am using galaxy for differential gene expression analysis. I first converted the ensembl GTF file by using the "Make Ensembl GTF compatible with Cufflinks" workflow. I used the converted annotation file for cufflinks and cuffmerge analysis, followed by cuffdiff. I noticed that the gene_id was chan ...
galaxy cufflinks gff written 2.7 years ago by Fang,Xiefan30 • updated 2.7 years ago by Jennifer Hillman Jackson23k
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Answer: A: RNA-seq analysis in Galaxy
... I figured out the problems regarding the annotation file. It turns out that I need to convert the ensembl GTF file by using the "Make Ensembl GTF compatible with Cufflinks" workflow. I used the converted annotation file for cufflinks and cuffmerge. I got the read counts and fold changes after cuffdi ...
written 2.7 years ago by Fang,Xiefan30
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RNA-seq analysis in Galaxy
... I am doing RNA-seq analysis for several mouse samples and I encounter problems during differential expression analysis. First, I used Galaxy tools to clean,filter, and trim my reads and Tophat for alignment. I selected the built-in genome mm10 for alignment and the mapping efficient is above 85%. Th ...
galaxy rna-seq cufflinks tool gff written 2.7 years ago by Fang,Xiefan30
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How To Merge Fastq Groomer Files In Galaxy?
... Dear Galaxy users, Does anyone know how to merge several FASTQ groomer files by using Galaxy? If not, is there any other program that can achieve this? The size of one FASTQ groomer file is around 1GB. Thank you! Best regards, Xiefan Fang, Ph.D. Postdoctoral associate Department of Pedia ...
galaxy written 5.2 years ago by Fang,Xiefan30 • updated 5.2 years ago by Peter Cock1.4k

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