User: sv112

gravatar for sv112
sv11210
Reputation:
10
Status:
New User
Location:
United States
Last seen:
2 years, 7 months ago
Joined:
2 years, 8 months ago
Email:
s****@duke.edu

Posts by sv112

<prev • 5 results • page 1 of 1 • next >
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Answer: A: Blank Cufflinks output
... Hi Jen, Thanks for the response. I went back and replaced my .gff  annotation file with a different one bearing a .gtf extension. Strangely, that seems to have fixed the problem! Maybe the gff file was corrupted, or wasn't being read properly by the newer version of Cufflinks. I am a little surpris ...
written 2.6 years ago by sv11210
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Blank Cufflinks output
... Hi! I am conducting an RNA-seq analysis with Saccharomyces cerevisiae-derived data. In my workflow, I am using the 'TopHat accepted hits' BAM output files as input for a downstream Cufflinks analysis on the main Galaxy server online. All of my Cufflinks outputs, however, are coming out blank(i.e no ...
cufflinks s.cerevisiae rna-seq written 2.6 years ago by sv11210
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Answer: A: S.cerevisiae reference genome from USCS--2bit extraction issue
... That worked perfectly, thanks! Regards, Sri ...
written 2.7 years ago by sv11210
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S.cerevisiae reference genome from USCS--2bit extraction issue
... I extracted the SacCer3 (S.cerevisiae) reference genome sequence from the corresponding 2bit file that I downloaded from USCS, via the TwobitTofa utility. However, I only see the sequence of chromosome I when I open the file. What is the specific command to convert all the data in the 2bit file into ...
2bit tools fasta download written 2.7 years ago by sv11210 • updated 2.7 years ago by Jennifer Hillman Jackson23k
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Saccharomyces cerevisiae reference genome for TopHat,Bowtie
... Hi, I am new to Galaxy, and for my first project I wish to analyze some sequences we recently obtained from an RNA-Seq experiment. I am stuck at the step of using TopHat/Bowtie for aligning my FASTQ files to a S.cerevisiae reference genome (preferably, S288C). The problem is that I don't see any S. ...
galaxy bowtie tophat rna-seq written 2.7 years ago by sv11210 • updated 2.7 years ago by Jennifer Hillman Jackson23k

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