HELP WITH PROJECT!!!!

Question: HELP WITH PROJECT!!!!

2.6 years ago by

So I need help with this project--> I already have my de novo assembly from the genomics workbench. However, I need a step by step tutorial for creating the bottom list:

Excel list with FPKM or other measure of expression for each contig (20 points).
Excel list of genes/contigs with significantly different expression between two biological replicates (20 points).
Provide a downstream analysis such as gene ontology or other type of analysis (20 points).

Please help me! I'm desperate!

rna-seq tophat bowtie cufflinks • 771 views

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modified 2.6 years ago by pinakin76 • 0 • written 2.6 years ago by gabriela.nine • 0

2.6 years ago by

Dannon Baker ♦ 3.7k

United States

Dannon Baker ♦ 3.7k wrote:

Here's a recent tutorial by Anton which will walk you through reference-based rna-seq:
https://github.com/nekrut/BMMB554/wiki/10.-Reference-based-RNA-seq

This definitely differs a bit from your school project, which appears to be de novo, but it might be useful background information to help get you started.

ADD COMMENT • link written 2.6 years ago by Dannon Baker ♦ 3.7k

2.6 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This is our RNA-seq tutorial. https://wiki.galaxyproject.org/Learn/GalaxyNGS101#Reference-based_RNA-seq

To learn Galaxy in general, please see: http://usegalaxy.org/galaxy101

Any output in tabular format can be filtered with tools like Filter and Select. This can be downloaded and imported into Excel.

For downstream analysis, there are many choices. Search by keywords to find tools ("gene ontology", etc). Make sure they are appropriate for RNA-seq (not Variant analysis). Usage is on the tool forms and there are practical examples in the second tutorial linked above.

For example, use common gene name identifiers in the results to associate content with external data sources using tools like "Join two Datasets/Compare two Datasets". This method will only work if you incorporate an appropriate reference annotation in Cuffdiff. iGenomes is one good source for reference annotation. There are many posts on this forum about RNA-seq annotation and the capture of gene ids - a search will find them.

Best, Jen, Galaxy team

ADD COMMENT • link modified 2.6 years ago • written 2.6 years ago by Jennifer Hillman Jackson ♦ 25k

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