User: k.ip

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k.ip10
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New User
Location:
Australia
Last seen:
6 months ago
Joined:
3 years, 2 months ago
Email:
k***@garvan.org.au

Posts by k.ip

<prev • 7 results • page 1 of 1 • next >
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RNA-seq data normalisation with housekeeping genes
... Hi there, I just generated a couple of RNA-seq dataset hoping to identify the differentially expressed genes caused by a particular treatment, for instance, 4 weeks of High fat diet treatment. So I have used the standard procedures to analyze the data such as TopHat, cufflinks, and cuffdiff to id ...
normalization galaxy rna-seq written 14 months ago by k.ip10 • updated 14 months ago by Jennifer Hillman Jackson25k
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Is it important to perform Adapter sequence removal step?
... Hello, Can I ask is it important to perform the adapter removal step, when I ran the RNA-seq fastq file with FastQc and it didn't pick up any over-represented sequences? And how would I know what is the adapter sequences from my data file? Thanks a lot for answering me. Kind regards, Ken ...
rna-seq written 2.2 years ago by k.ip10 • updated 2.2 years ago by Devon Ryan1.9k
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Answer: A: Different RNA-seq result when I look at the gene_differential file and the trans
... Hi Jen and Mo, Thank you so much for explaining this to me clearly! You guys are very helpful. Thanks and regards, Ken ...
written 2.2 years ago by k.ip10
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Different RNA-seq result when I look at the gene_differential file and the transcript_differential file generated by cuff-diff
... Hi, I am wondering what is the exact difference between the gene list of the **transcript differential expression testing file** and the **gene differential expression testing file** generated by cuffdiff? The reason I ask this is because I found a lot of genes were not tested in the transcript d ...
rna-seq written 2.2 years ago by k.ip10
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Answer: A: Using different reference genome yields different results in RNA-seq data analys
... Your explanation is very clear and helpful! Thank you so much.  ...
written 3.2 years ago by k.ip10
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Using different reference genome yields different results in RNA-seq data analysis
... Hello, I've got some questions with my RNA-seq results generated by galaxy.  For the experiment, I have a control group and a KO group (n=3), and I tried to look at the differential expressing genes between the two.  For data processes, i just simply mapped my reads back to the mm10 mouse genome, ...
galaxy rna-seq written 3.2 years ago by k.ip10
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What is the purpose of Cufflink and Cuffmerge?
... Hi guys, I am new to the galaxy server, and I want to analyse my RNA-seq data with the following standard pipeline (TopHat=>Cufflinks=>Cuffmerge=>Cuffdiff) to determine differential expression between control and treatment group. However, both cufflink and cuffmerge only generate GTF file ...
bam galaxy cufflinks rna-seq written 3.2 years ago by k.ip10 • updated 3.2 years ago by Jennifer Hillman Jackson25k

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Popular Question 2.2 years ago, created a question with more than 1,000 views. For What is the purpose of Cufflink and Cuffmerge?

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