README

This database and information system is designed to integrate resources from the wheat community. The initial targets are to integrate:

• Genetic maps
• Genome assemblies
• SNP Markers
• Syntenic genes
• Gene anottation
• PolyMarker

Architecture

The general components in the system are stacked as follow: Note: The BAM files may be scrollable.

Database

Use case

This are the initial use cases

Setting up

Once the database is setup via rake db:migrate there are rake tasks to add teh data. If you want to clear the database, to clear the data during development: rake db:drop db:create db:migrate

Adding the list of markers

In order to add the markers, a table with a marker per row, with all the names for the marker and a column with the sequence is used as input. The only column not treated as a name is the column with the header "Sequence", which contains the sequence for the SNP within brackets, with the IUAPC ambiguity code representing the different alleles in the SNP. Example:

Affymetrix_Code,Bristol_Affy_Code,Bristol_SNP_Code,Bristol_Contig_Code,Sequence
AX-94381124,BA00222391,No BS code,GJKKTUG01CGTKM_219,CTGTAGATGTGCACCTTGATGGTATCCTCGGCGATGAGCTCGAAGACGCA[R]ACNTCGAACTTCTCCAGATTGTTGCCGATCGAGAACTGGCTCCAGCCTCT
AX-94381126,BA00232763,No BS code,FZU8VVO01APRT5_148,ACAACCCGTGGTGGAAATAAGCGACGCAAGCTCCGGCAGCAATGCTCACT[Y]GNGTGATATGTTAAGCCTCCTGCCCAGTCCTAAGAACGCTGCTATAAGAC
AX-94381127,BA00233916,No BS code,contig77177_250,GCGTCCCCGGCCGCCACAACGGCCATCGCGGTCGGCGACCGGCTCCCCGA[M]NCGACGCTCTCCTACTTCGACGCCCCCGACGGCGAGCTGAAGACGGTGAC
AX-94381128,BA00235611,No BS code,GJKKTUG02JAI6G_371,TCGGTACTTCTTAAGACCAGTCTAGATGTTGCATATGAACATGAATCAAT[Y]GGGGTNACGCACATCATCAACAGATGATGTCACAATAAGAGTGGAGAGAG
AX-94381129,BA00239105,No BS code,contig78690_277,CCCCCAGTGAAAGGGAGCAGCCATTGACAGGCAAGGGCGAAGGAAGCAGC[R]ACGGNGCAGAACAAGACAGAGAGCAGGGGGCATGGGGGAGAAGGCTGCGG
AX-94381131,BA00249777,No BS code,contig82171_572,ACGGCCTCGTCAACTTCGACGAGTTCGTCAGGATGATGATGCTCTCCGAC[K]CCGACNNNNNNNNNNNNNNNNNTTGAGAGTCTGTCCGAGATAGATATATA
AX-94381137,BA00325640,No BS code,contig94834_761,AGTCGCTCATCGACAACGGCATCCACGTCAAGCTCTACCTCGACTGATCC[Y]TTTTCNNNNNNNNGCTGTGGTATGTCTGTTGCCGCTCTGCTTTCGACACC
AX-94381138,BA00327658,No BS code,contig94085_155,GGTGCCCTTGCTCCCCATCCTCCTCCTCCTCGCGCTGCTCTCGCCGGCCG[Y]CCGNGGCTCGGAGTCGCCGCAGTACGCGACGGTGCACGCGGAGTCGGACT
AX-94381140,BA00343181,No BS code,F0Z7V0F01DPY86_337,ATATTTGCTGTTTTCTTCAGTCTACCAGGCCGCTATGAAGCATTGTGGAA[R]GNGGTTGATGGTGTCAAGCAGCTTTGGAAGAACAGGAAGGAGCTCAAGGT

To load the markers in hte previous file, the following task is used:

rake marker:load_marker_from_820k_csv[820k_markers,data/head_affy.csv]

The first argument is the name of the marker set and the second the path with the csv. By default, the main name of the marker is the column Bristol_Affy_Code, but if it is missing, it defaults to the first name.

Adding a genetic map

rake "genetic_map:add[:name,:filename,:description,:species]"

• :name The name of the genetic map
• :filename A tab separated column, with four columns ID[string], Chromosome[string], position cM[float], order[int]

Example:

Ra_c23068_380 1A 0 1
BobWhite_c48447_529 1A 33.01 2
BS00062658_51 1A 37.14 3
BS00026003_51 1A 38.46 4
BS00071289_51 1A 42.4 5
Excalibur_c9509_1180 1A 42.4 6
GENE-0412_338 1A 42.4 7
IAAV3919 1A 42.4 8
Kukri_c18951_853 1A 42.4 9
RAC875_c42700_264 1A 42.4 10

• :description A short description of the genetic map, may include a doi
• :species The name of the species. It is optional. Defaults to Hexaploid Wheat

Adding the marker alignment to scaffolds

To load the positions of the markers, PSL alignments from Blat can be used. Only continous alignments are recorded.

rake marker:load_blat_position[data/all_sequences_bristol.psl,IWGSC1,82k_markers]

Adding Ensembl genes

A task to load genes crom the cdnas from Ensembl is provided. To load the data use the task:

rake genes:ensembl_genes[IWGSC2,Triticum_aestivum.IWGSC2.26.cdna.all.fa]

Adding mutations

The expected header of the file is:

Scaffold chromosome Library Line position chromosome position ref_base wt_base alt_base het/hom wt_cov mut_cov confidence Gene Feature Consequence cDNA_position CDS_position Amino_acids Codons SIFT score The order is important,