User: ctoscano

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ctoscano0
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2 years, 8 months ago
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2 years, 8 months ago
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c*******@purdue.edu

Posts by ctoscano

<prev • 7 results • page 1 of 1 • next >
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Comment: C: Cufflinks options to get similar results
... Thanks for your response Jen. Yes, I'm struggling with the max-bundle-length and I'm not sure wich Max Intron Length should I use. ...
written 2.7 years ago by ctoscano0
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Cufflinks options to get similar results
... Hello everyone, I'm trying to reproduce the results from a dataset from RNAseq I found on GEO. After I processed with the standard options on everything the FPKM values are a little higher. I noticed that in cufflinks I have different values, in their output file they have this command line:  cuf ...
galaxy cufflinks written 2.7 years ago by ctoscano0 • updated 2.7 years ago by Jennifer Hillman Jackson25k
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Answer: A: Each sample as a condition? - cuffdiff
... Well I want to get a condensed FPKM table with each sample on it, thats why I want to run the samples separetaly. I'll run cuffdiff with each condition for the differential expressed genes too.  ...
written 2.7 years ago by ctoscano0
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Each sample as a condition? - cuffdiff
... Hello everyone, I've been having doubts about running each sample as a condition to get the FPKM trancking file as a table with all of the results and not the condesed one for each condition. Is is possible? Can it generate errors? Thanks. ...
galaxy cufflinks written 2.7 years ago by ctoscano0
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Comment: C: Cufflinks and gene name
... I dowloaded the mm10 form iGenomes, used de UCSC version. I don't know wich GTF file to use, there's 4 folders with different dates. Should I use the latest?  Thanks! ...
written 2.7 years ago by ctoscano0
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Comment: C: Cufflinks and gene name
... Thank you Jen, I will try first with the GTF from iGenomes. ...
written 2.7 years ago by ctoscano0
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Cufflinks and gene name
... Hellos everyone, I know there's many posts regarding this question but I still have found myself unable to solve this problem. After processing with TopHat (reference genome mm10) and cufflinks with standard options, I try to use cuffmerge and cuffdiff to get FPKM values. I've used many different G ...
cufflinks galaxy written 2.7 years ago by ctoscano0 • updated 2.7 years ago by Jennifer Hillman Jackson25k

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