Details
-
Type:
Task
-
Status: Closed (View Workflow)
-
Priority:
Major
-
Resolution: Done
-
Affects Version/s: None
-
Fix Version/s: None
-
Labels:None
-
Story Points:2
-
Epic Link:
-
Sprint:Spring 3, Spring 4
Description
GOAL: To find highly similar protein cluster via CDHIT.
Need to see if this is a module already on the cluster.
If not, need to figure out installation.
Need to create a script to run.
We run CDHIT on each Transdecoder run we produce.
Attachments
Activity
Successfully ran CD-HIT on our de novo contigs (filtered/unfiltered protein files from Transdecoder) with the 10 RALF proteins and the Dehydration-induced 19-like protein.
filtered results are found here: /projects/tomato_genome/fnb/dataprocessing/brandon_work/CD-HIT/RALF_with_denovo/filtered_contigs/results/filtered_varieties_merged.clstr
unfiltered results are found here:/projects/tomato_genome/fnb/dataprocessing/brandon_work/CD-HIT/RALF_with_denovo/unfiltered_contigs/results/unfiltered_varities_merged.clstr
We get at least one hit for all RALF proteins except SLRALF2.
Reran CD-HIT, but this time appended RALF proteins to end of our denovo protein fastas.
I ran transdecoder on our filtered and unfiltered contigs, so I also ran CDHIT on each. Summarizing cluster numbers in ticket 4113.
filtered results: /projects/tomato_genome/fnb/dataprocessing/brandon_work/CD-HIT/RALF_with_denovo/filtered_contigs/varieties_with_RALF/results
unfiltered results: /projects/tomato_genome/fnb/dataprocessing/brandon_work/CD-HIT/RALF_with_denovo/unfiltered_contigs/varieties_with_RALF/results
The results look good.
We need to look at these a bit more and break down the 26,000+ clusters. We can summarize these results as a figure.
But we might want to run these again as a new ticket, and explore -c option of 0.9. 90% sequence similarity. Can try both more stringent and less.
But that will be a new ticket.
This one is ready for closing.
Also include RALF proteins and the gene (in protein form) "Solyc01g100140.4.1:Dehydration-induced 19-like protein"