User: mariel.voutounou

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Posts by mariel.voutounou

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Counts vs FPKM
... I was able to retrieve the counts from my RNAseq analysis via Cuffdiff so as to compare with the FPKM values  Question 1) Please tell me what the decimal points in counts correspond to, because as is, i cannot make much sense of the data  e.g     WT                             TEST 5566.54357   ...
counts fpkm written 2.6 years ago by mariel.voutounou0
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Comment: C: Freeing usage space in Galaxy
... Begin forwarded message: From: Mariel Voutounou <mav3001@med.cornell.edu<mailto:mav3001@med.cornell.edu>> Subject: Galaxy Counts - decimals Date: August 31, 2015 at 10:27:45 AM EDT To: galaxystar+3e7c65fc+code@biostars.io<mailto:galaxystar+3e7c65fc+code@biostars.io> Dear Jen, Thank ...
written 2.6 years ago by mariel.voutounou0
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Comment: C: Freeing usage space in Galaxy
... Dear Jen, I was able to find the counts on the Cuffdiff tool form - My question now is what does the decimal point stand for? For example: Gene WT Test F2rl2 5566.54 10305.4 Kind Regards, Mariel Mariel Voutounou, Ph.D. Burke Medical Research Institute, Department of Ne ...
written 2.6 years ago by mariel.voutounou0
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Comment: C: Freeing usage space in Galaxy
... Jen, Thanks for the reply& suggestions. I will give it a go. Mariel ...
written 2.7 years ago by mariel.voutounou0
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Answer: C: Freeing usage space in Galaxy
... Dear Jennifer, I have another question in regards to Galaxy that you might be able to help me with. We usually get our Galaxy results in FPKM for each gene. What I would like to know is, if it is possible to also get the counts for each gene and if there is an easy way to do that. Thank you in adva ...
written 2.7 years ago by mariel.voutounou0
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Comment: C: Freeing usage space in Galaxy
... Hello Jen, Thank you for the swift response. in all cases that i have deleted data, I chose the permanent deletion. I just gave it another go - i permanently deleted a data set 111 GB big, but again no change - So indeed it doesn’t seem to delete them (even if I choose the permanent deletion and th ...
written 2.8 years ago by mariel.voutounou0
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Freeing usage space in Galaxy
... Hello,  I have reached a 94% usage space and I would to know how I could free up some space. I have already permanently deleted some past data - but that did not increase the current space.   Kind Regards,   Mariel  ...
space usage written 2.8 years ago by mariel.voutounou0 • updated 2.8 years ago by Jennifer Hillman Jackson24k
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Comment: C: p values don't match up
... Dear Jen, Thank you for your reply. I have done (as you recommended) a re-run of the analysis - I found the same results as my newest run -but i am still unsure about the parameters that you are referring to. Is it possible to know what these upgrades where? Is it the number of base pairs that are ...
written 3.4 years ago by mariel.voutounou0
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p values don't match up
... A college of mine run an RNA-seq analysis using Galaxy a couple of years ago. I used the same datasets to run a new analysis - and even though the list of genes generated was identical, I found discrepancies in the number of genes detected as significant (his dataset had more than a thousand signif ...
rna-seq written 3.5 years ago by mariel.voutounou0 • updated 3.5 years ago by Jennifer Hillman Jackson24k

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