How to analyze Genes Differential Expression using Galaxy? Thanks.

[byou678]

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!

[tnabtaf]

Does the material at this page help?:

http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise

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

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

[byou678]

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.

Does the material at this page help?:

http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise

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

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