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Hi Jen,
I use tophat to align the RNA-seq data, then use cufflink ,cuffcompare
and cuffdiff with a reference GTF fileto find differential expressed
non-coding RNA.
But I don't know what is non-coding RNA track in the output file s
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Hi everybody,
Maybe a dumb question but does someone know if we can use the aaChanges tool
on a custom genome? I have my SNP dataset and my gene dataset but I can only
assign them to one of the genome build already in UCSC... I am u
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Sure, no problem. Those estimates are indeed way off, ideally they're
within about 10% of the actual count. Would you mind sharing the
history with me at this email address so that I might take a look and
figure out where the es
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Hi Dannon,
Thanks for telling me about that count tool. I had not used it before. So,
it seems the line estimates in the history windows are a bit screwy. One
pileup file I mentioned estimated ~4,000,000 lines and the count tool
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As a first step, please confirm an exact line count for the files. See the
"Line/Word/Character count" tool in the Text Manipulation section to do this.
If the estimate is significantly off, please share the history with me and I
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Hello,
I am curious if the line estimation shown in the history window for pileup
generation is at all accurate. I am using the pileup files to generate
expression data from bwa mapping for looking at differential expression, but
I
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Can someone help me understanding the quartile normalization in Cufflinks? I
read different threads in which they reported that the FPKM values were
inflated after normalization (-N) but most people didn't report their values
so I do
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Hello,
Without seeing your work history, it is difficult to know exactly which
steps/options are being used with the RNA-seq tools. However, I can let
you know t
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cross-post
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Original Message
Subject: Re: [galaxy-dev] [galaxy-user] Cuffdiff question about using an
unspecified (?) database/build
Date: Thu, 25
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Dear all,
I use cuffdiff in galaxy net version. The output are isoform.diff , gene.diff
...etc, but I want to find the differential expressed non-coding RNAs. How can
I get these information?
Thank you
Chen Yao
___
===> Please use "Reply All" when responding to this email! <===
Dear all,
I use cuffdiff in galaxy net version. The output are isoform.diff , gene.diff
...etc, but I want to find the differential expressed non-coding RNAs. How can
I get these information?
Thank you
Chen Yao
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