New Informatics Initiatives
(in order of priority
)
run the following through pipeline (with documentation)
4 Paired-End Gonad Libraries
http://eagle.fish.washington.edu/whale/index.php?dir=Friedman_Oly_broodstock%2Ffull%2F
http://eagle.fish.washington.edu/whale/Friedman_Oly_broodstock/full/filtered_108A_Male_Mix_AGTCAA_L004_R2.fastq.gz
http://eagle.fish.washington.edu/whale/Friedman_Oly_broodstock/full/filtered_108A_Male_Mix_AGTCAA_L004_R1.fastq.gz
http://eagle.fish.washington.edu/whale/Friedman_Oly_broodstock/full/filtered_108A_Female_Mix_GGCTAC_L004_R2.fastq.gz
http://eagle.fish.washington.edu/whale/Friedman_Oly_broodstock/full/filtered_108A_Female_Mix_GGCTAC_L004_R1.fastq.gz
http://eagle.fish.washington.edu/whale/Friedman_Oly_broodstock/full/filtered_106A_Male_Mix_TAGCTT_L004_R2.fastq.gz
http://eagle.fish.washington.edu/whale/Friedman_Oly_broodstock/full/filtered_106A_Male_Mix_TAGCTT_L004_R1.fastq.gz
http://eagle.fish.washington.edu/whale/Friedman_Oly_broodstock/full/filtered_106A_Female_Mix_GATCAG_L004_R2.fastq.gz
http://eagle.fish.washington.edu/whale/Friedman_Oly_broodstock/full/filtered_106A_Female_Mix_GATCAG_L004_R1.fastq.gz
- Setup public facing iPython Notebook install on hummingbird.
I would like to setup IPython notebook server on hummingbird that could access and run remotely.
http://ipython.org/ipython-doc/dev/interactive/htmlnotebook.html
- Install implement De-novo assembly / RNA_seq pipeline locally....
http://khmer-protocols.readthedocs.org/en/v0.8.2/mrnaseq/index.html
using DH3 BB3 as models
- see sheet f
or raw data.
- Setup full installation of Galaxy.
Currently we have Galaxy server running on genefish.fish.washington.edu.
It functions but is missing several tools / dependancies.
http://wiki.galaxyproject.org/Admin/Get%20Galaxy
We would like something more robust with complete complement.
Essentially I think we would like the production environment install on bigfish.
http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer
It might be just easier to upgrade what we have?
- De Novo assembly of
Ostrea lurida
transcriptome
combine all into master transriptome
Below is reads we have to date:
Version 1 raw reads (used in
http://goo.gl/roshW
)
http://eagle.fish.washington.edu/cnidarian/filtered_400_NoIndex_L006_R1.fastq.gz
http://eagle.fish.washington.edu/cnidarian/filtered_2000_NoIndex_L007_R1.fastq.gz
OA larval data
http://eagle.fish.washington.edu/cnidarian/filtered_400_GTCCGC_L004_R1.fastq.gz
http://eagle.fish.washington.edu/cnidarian/filtered_1600_GTGGCC_L004_R1.fastq.gz
http://eagle.fish.washington.edu/cnidarian/filtered_1000_GTGAAA_L004_R1.fastq.gz
http://eagle.fish.washington.edu/cnidarian/filtered_2200_GTTTCG_L004_R1.fastq.gz
Single End Gonad data
http://eagle.fish.washington.edu/cnidarian/filtered_106A_Female_Mix_GATCAG_L007_R1.fastq.gz
http://eagle.fish.washington.edu/cnidarian/filtered_106A_Male_Mix_TAGCTT_L007_R1.fastq.gz
http://eagle.fish.washington.edu/cnidarian/filtered_108A_Male_Mix_AGTCAA_L007_R1.fastq.gz
http://eagle.fish.washington.edu/cnidarian/filtered_108A_Female_Mix_GGCTAC_L007_R1.fastq.gz
4 Paired-End Gonad Libraries
http://eagle.fish.washington.edu/whale/index.php?dir=Friedman_Oly_broodstock%2Ffull%2F
http://eagle.fish.washington.edu/whale/Friedman_Oly_broodstock/full/filtered_108A_Male_Mix_AGTCAA_L004_R2.fastq.gz
http://eagle.fish.washington.edu/whale/Friedman_Oly_broodstock/full/filtered_108A_Male_Mix_AGTCAA_L004_R1.fastq.gz
http://eagle.fish.washington.edu/whale/Friedman_Oly_broodstock/full/filtered_108A_Female_Mix_GGCTAC_L004_R2.fastq.gz
http://eagle.fish.washington.edu/whale/Friedman_Oly_broodstock/full/filtered_108A_Female_Mix_GGCTAC_L004_R1.fastq.gz
http://eagle.fish.washington.edu/whale/Friedman_Oly_broodstock/full/filtered_106A_Male_Mix_TAGCTT_L004_R2.fastq.gz
http://eagle.fish.washington.edu/whale/Friedman_Oly_broodstock/full/filtered_106A_Male_Mix_TAGCTT_L004_R1.fastq.gz
http://eagle.fish.washington.edu/whale/Friedman_Oly_broodstock/full/filtered_106A_Female_Mix_GATCAG_L004_R2.fastq.gz
http://eagle.fish.washington.edu/whale/Friedman_Oly_broodstock/full/filtered_106A_Female_Mix_GATCAG_L004_R1.fastq.gz
- Examine Oly PacBio Data
Data @
http://eagle.fish.washington.edu/whale/index.php?dir=Pat%2F
Complete
- Transfer Coordinate System from Genome to Transcriptome
Solution:
https://github.com/uwescience/sqlshare/wiki/Workflow:-Transfer-Coordinates-from-Genome-to-Transcriptome