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Old 09-26-2011, 09:01 AM   #1
byou678
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Location: Maryland

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Default How to analyze Genes Differential Expression using Galaxy? Thanks.

Hi All,

Now I have two Paired-End samples data ( they are Next Generation Sequence Data and fastq format) generated from Illumina GA II. Let's say Data Lane1 and Data Lane2. After Quality trimming and Adapter trimming, I want to check the Genes Differential Expression between these two samples. How could I do that in Penn State version Galaxy or other versions with only having Reference File?

With Ratsch Lab Version Galaxy, I know I can use DESeq (determine differentially expressed transcripts form read alignments) if I have the Annotation File.

Any info is welcome and Thanks a lot in advance!
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Old 09-26-2011, 04:03 PM   #2
tnabtaf
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Does the material at this page help?:

http://main.g2.bx.psu.edu/u/jeremy/p...lysis-exercise

You can also post this question to the galaxy-user mailing list:

http://galaxyproject.org/wiki/Mailing%20Lists
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Old 09-27-2011, 09:03 AM   #3
byou678
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Thanks for your help, tnabtaf!

However I don't have the Annotation file. And I think I can generate pileup file from BAM dataset, then use PILEUP COUNTS ( Pileup Compare counting reads mapped per reference sequence) to get a Counts Table about these two samples. Next I may use this Table to check differentially expressed genes in other software, like R. Any other idea? Thanks.

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Originally Posted by tnabtaf View Post
Does the material at this page help?:

http://main.g2.bx.psu.edu/u/jeremy/p...lysis-exercise

You can also post this question to the galaxy-user mailing list:

http://galaxyproject.org/wiki/Mailing%20Lists
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