Hannah's+notebook


 * __April 01, 2014__**
 * __taxonomic representation of OlyO transcriptome v3 cdd blast through galaxy__**
 * uploaded cdd blast file
 * "fetch taxonomic data"
 * **Phylum** || **Counts** ||
 * Chordata || 12403 ||
 * Proteobacteria || 1433 ||
 * Streptophyta || 1111 ||
 * Firmicutes || 767 ||
 * Arthropoda || 434 ||
 * Ascomycota || 427 ||
 * Euryarchaeota || 281 ||
 * Echinodermata || 104 ||
 * Cyanobacteria || 82 ||
 * Basidiomycota || 65 ||
 * Apicomplexa || 60 ||
 * Chlamydiae || 47 ||
 * Annelida || 38 ||
 * **Mollusca** || **38** ||
 * Bacteroidetes || 30 ||
 * Tenericutes || 26 ||
 * Spirochaetes || 22 ||
 * Chlorophyta || 17 ||
 * Deinococcus-Thermus || 17 ||
 * Platyhelminthes || 16 ||
 * Crenarchaeota || 7 ||
 * Euglenida || 4 ||
 * Nematoda || 3 ||
 * Cnidaria || 2 ||
 * Neocallimastigomycota || 2 ||
 * Porifera || 1 ||
 * Tree:**


 * __March 27, 2014__**

-OlyO Transcriptome v2 as reference genome -min read length fraction: 0.9 -max hits per read: 10
 * Parameters on the RSeq Analysis:**

-unpaired two group comparison -set expression value to unique gene reads
 * Parameters in Expression Analysis:**

Info for annotating genome and location of GOSlim database http://oystergen.es/query https://github.com/uwescience/sqlshare/wiki/Workflow:-Annotating-Oyster-Genes


 * __February 18, 2014__**
 * found non-integer!!
 * Olurida_trim_nodups_v2reads_contig_56245 102 0.015 (old)
 * Olurida_trim_nodups_v2reads_contig_56245 1 3102 (corrected)
 * working with RNA-Seq Analysis files for 108 male/female broodstock data and 106 male/female broodstock data <-- looking at unique gene reads
 * converted CLC files into text files through iPython
 * ran DESeq script on the new text files through R
 * constructed data plots for each file

Plots: [|Scatter of 106 male/female unique gene reads] [|Histogram of 106 male/female unique gene reads] [|Scatter of 108 male/female unique gene reads] [|Histogram of 108 male/female unique gene reads]

data table for[| 106 Broodstock] data table for [|108 Broodstock]


 * __January 28, 2014__**
 * ran RNA-Seq Analysis on OlyO broodstock data


 * __January 21, 2014__**
 * All files in CLC moved to CLC_local_bird --> Hannah
 * Uploaded male and female data to iPlant and Galaxy
 * also uploaded OlyO transcriptome to iPlant and Galaxy


 * __January 07, 2014__**
 * Sequence ID, GOID, and SPID for swissprot OlyO data into excel files- includes data charts
 * in files on eagle under folder named "Hannah"
 * Olympia oyster transcriptome fasta file uploaded to CLC workbench under folder named "Hannah"
 * filtered female 106A OlyO paired data through NGS import
 * file NGS Raw Data --> Friedman Broodstock --> full
 * filtered male 106A OlyO paired data through NGS import (same file location as above)
 * filtered female 108A OlyO paired data through NGS import (same file location as above)
 * filtered male 108A OlyO paired data through NGS import (same file location as above)

Many of the blasts were not fully completed so they must be redone. Re-doing failed blasts on the following databases: Blasts using cdd_delta (Oly Blast 2) and refseq_rna (Oly Blast 10) have successfully completed
 * __October 16, 2013__**
 * refseq_protein (Oly Blast 1)
 * env_nr (Oly Blast 5)
 * uniprot_swissprot (Oly Blast 12)

I have been having issues with the vector and pdbaa databases not blasting.
 * __October 10, 2013__**


 * __October 9, 2013__**

(list last revised 10/10/2013) Blast databases tried:
 * cdd_delta
 * env_nr
 * est_others
 * nr
 * nt
 * refseq_genomic
 * refseq_protein
 * refseq_RNA
 * env_nt
 * uniprot_swissprot

Blast databases not tried:

Databases with Issues
 * vector
 * pdbaa
 * swissprot

Running some more data through blast- added to the list on October 1st.
 * __October 3, 2013__**

Reminder: DIfferent Blasts
 * blastn: search **nucleotide** database using **nucleotide** query
 * tblastn: search a **translated nucleotide** database using a **protein** query
 * blastx: search a **protein** database using a **translate nucleotide** query
 * tblastx: search a **translated nucleotide** database using a **translated nucleotide** query
 * blastp: search a **protein** database using a **protein** query

Remember- to find notebook on iPython type //ipython notebook --pylab inline// into the terminal

d-128-95-149-219:~ srlab$ cd /Volumes/web/scaphapoda/Hannah

d-128-95-149-219:Hannah srlab$ pwd

/Volumes/web/scaphapoda/Hannah

d-128-95-149-219:Hannah srlab$ ipython notebook -pylab inline

Google Doc of [|BLAST Databases]

Continuing blasting Oly transcriptome against various databases in whale folder
 * __October 1, 2013__**

Program **blastx** works for the following databases:
 * refseq_protein (output in Oly_Blast_1)
 * cdd_delta (output in Oly_Blast_2)
 * env_nr (output in Oly_Blast_5)
 * nr (output in Oly_Blast_8)

Program **blastn** works for the following databases:
 * refseq_genomic (output in Oly Blast 4)
 * est_others (output in Oly_Blast_7)
 * refseqgene (output in Oly Blast 9)
 * refseq_rna (output in Oly Blast 10)

Ran blast yesterday (September 25) on Olympia oyster data comparing against new databases. Continuing blast sequences today.
 * __September 26, 2013__**

Learning more about IPython and SQLshare
 * __September 24, 2013__**

__Changing | to tabs in IPy:__ !tr '|' "\t"  /Volumes/web/scaphapoda/Hannah/OlyO_trans_v3_swissprot_mod.txt

__Joining Tables in SQLshare:__ SELECT * FROM [wearh@washington.edu].[OlyO_trans_v3_swissprot_mod.txt] oly left join [sr320@washington.edu].[associations_uni_swisspro_012410] des on oly. Column3 = des. ID

Steven showed me how to run IPython and BLAST What was ran: !blastx -query /Volumes/web/scaphapoda/Hannah/Olurida_transcriptome_v3.fasta -db /Users/Shared/Apps/ncbi-blast_28/db/uniprot_sprot -out /Volumes/web/scaphapoda/Hannah/Olur_blast_sprot.txt -outfmt 6 -evalue 1E-5 -max_target_seqs 1 -num_threads 14
 * __September 18, 2013__**

Program: blastx Language: -query (file) Database: -db (file: /Users/Shared/Apps/ncbi-blast_28/db/uniprot_sprot) Output Location: -out (new file in .txt format) Other Info: -outfmt 6 -evalue 1E-5 -max_target_seqs 1 -num_threads 14


 * __September 5, 2013__**
 * Took tissue samples from** breeding group SN 9 and SN 30**.**

Group SN 9**
 * mortality: 7/20
 * samples in this group labeled SN_26A,B,C through SN_38A,B,C
 * mantle tissue in samples A and B
 * adductor tissue samples in samples C


 * Group SN 30**
 * mortality: 7/18
 * samples in this group labeled SN_39A,B,C through SN_49A,B,C
 * mantle tissue in samples A and B
 * adductor tissue samples in samples C

All of the breeding group oysters from NF, HL, and SN have been sampled. Tissue samples were placed in storage nine boxes and labeled according to the contents: NF_A, NF_B, NF_C, HL_A, HL_B, HL_C, SN_A, SN_B, and SN_C.

Took tissue samples from **breeding group SN 15 and SN 21**.
 * __September 4, 2013__**


 * Group SN 15**
 * mortality: 7/20
 * samples in this group labeled SN_1A,B,C through SN_13A,B,C
 * mantle tissue in samples A and B
 * adductor tissue samples in samples C


 * Group SN 21**
 * mortality: 5/17
 * samples in this group labeled SN_14A,B,C through SN_25A,B,C
 * mantle tissue in samples A and B
 * adductor tissue samples in samples C

Took tissue samples from **breeding group HL 19**. One of the oysters was much larger than the rest of the Hood Canal oysters sampled- about 2.5 inches length opposed to 1 inch length
 * __August 22, 2013__**
 * mortality: 1/16
 * samples in this group labeled HL_50A,B,C through HL_64A,B,C
 * mantle tissue in samples A and B
 * adductor tissue samples in samples C

Took tissue samples from **breeding group HL 16**.
 * __August 15, 2013__**
 * mortality: 1/18
 * samples in this group labeled HL_33A,B,C through HL_49A,B,C
 * mantle tissue in samples A and B
 * adductor tissue samples in samples C

Took tissue samples from **breeding group HL 28**. One of the oysters was much larger than the rest of the Hood Canal oysters sampled- about 2.5 inches length opposed to 1 inch length Shells from breeding group HL 4 were dried, labeled corresponding the tissue sample number and placed in individual plastic bag.
 * __August 09, 2013__**
 * mortality: 6/19
 * samples in this group labeled HL_19A,B,C through HL_32A,B,C
 * mantle tissue in samples A and B
 * adductor tissue samples in samples C

Started taking samples from a new breeding group: Hood Canal (HL). Took mantle and adductor muscle tissue samples from **breeding group HL 4**. Found bags for all the dried oyster shells! They are now individually labeled and bagged.
 * __August 08, 2013__**
 * mortality: 2/20
 * samples in this group labeled HL_1A,B,C through HL_18A,B,C
 * mantle tissue in samples A and B
 * adductor tissue samples in samples C

Sampled the last group of North Sound Fidalgo Bay. Oysters were frozen so they were placed in a water bath to thaw. Took mantle and adductor tissue samples from breeding group **NF #?** Dried shells from NF 8 were labeled corresponding to the tissue sample number.
 * __August__** **__06, 2013__**
 * Samples are labeled as NF_60A,B,C through NF_78A,B,C
 * mortality: 0/19

Took mantle and adductor tissue samples from breeding group **NF 8**. Dried shells from NF 14 were labeled corresponding to the tissue sample number.
 * __July 31, 2013__**
 * Samples are labeled as NF_41A,B,C through NF_59A,B,C
 * mortality: 0/19

Oyster shells from group NF 14 were labeled by writing the group and sample number directly onto the shell once dry. All oyster shells from the breeding groups will continue to be labeled in this same manner. Took mantle and adductor tissue samples from oysters in group **NF 20.**
 * __July 30, 2013__**
 * Samples are labeled as NF_21A,B,C through NF_40A,B,C
 * mortality: 0/19

Since the commercial oyster mantle tissue samples were being stored in snap lid capsules, they needed to be better preserved so we separated the A and B samples into containers and vacuum sealed them. Started collecting tissue samples from oyster breeding groups. The same methods as described previously were used to collect two samples of mantle tissue per oyster in addition to a sample of adductor muscle from each oyster. The mantle tissues were labeled as NF#A and NF#B, and all adductor tissue samples were labeled as NF#C. Breeding group NF14 contained 20 live oysters (all sampled) and zero dead/un-sampled oysters. The oyster shells from NF14 were labeled corresponding to the tissue sample number and left to dry out for future research.
 * __July 25, 2013__**
 * Breeding Group NF14 Olympic Oyster Tissue Samples**

Finished sampling the commercial Olympic oysters that were collected last December, 2012. There were 142 oysters that tissue was extracted from with two samples per oyster (labeled A and B).
 * __July 23, 2013__**

Continued to collect mantle tissue samples from Olympic oysters using the same procedure as described on July 28, 2013. Collected 52 tissue samples and starting to get a better understanding of oyster anatomy.
 * __July 19, 2013__**

First day in the lab! Took mantle tissue of commercial raised adult Olympic oysters (//Ostreola conchaphila//) for DNA extraction. Oysters were sliced open by prying apart the shells at the hinge and then severing the abductor muscle to reveal the internal organs. Two tissue samples from the mantle of each oyster were taken and placed into separate snap cap tubes with a 70% ethanol solution. Forceps and tweezers used to extract the tissue sample were sanitized after each oyster in a alconox, bleach, and water bath process to avoid DNA contamination. 64 tissue samples were collected.
 * __July 18, 2013__**
 * Olympic Oyster Mantle Tissue Samples**