Thursday Jan 2

ApTranscriptome

Each BLAST script completed in average of about 2 hours (min 35 minues, max 4hr30min) using 30 threads!

Quick check that all transcripts BLASTed:

tg-johnsg@Mason: /N/dc2/scratch/tg-johnsg/ncbi_nr> grep -c “AphVT” AphVTsub*_blastx2nrinsecta AphVTsub10_blastx2nrinsecta:5001 AphVTsub11_blastx2nrinsecta:5001 AphVTsub12_blastx2nrinsecta:5001 AphVTsub13_blastx2nrinsecta:5001 AphVTsub14_blastx2nrinsecta:5001 AphVTsub15_blastx2nrinsecta:5001 AphVTsub16_blastx2nrinsecta:5001 AphVTsub17_blastx2nrinsecta:5001 AphVTsub18_blastx2nrinsecta:4647 AphVTsub1_blastx2nrinsecta:5001 AphVTsub2_blastx2nrinsecta:5001 AphVTsub3_blastx2nrinsecta:5001 AphVTsub4_blastx2nrinsecta:5001 AphVTsub5_blastx2nrinsecta:5001 AphVTsub6_blastx2nrinsecta:5001 AphVTsub7_blastx2nrinsecta:5001 AphVTsub8_blastx2nrinsecta:5001 AphVTsub9_blastx2nrinsecta:5001

blastgo

Working through example with Blast2GO program.

Notes:

BLAST step - runs BLAST and retrieves top 20 hits by default
Mapping - determines best blast hit based on a number of criteria…
Annotation - extracts and reports GO terms for mapped hit
- note that GO terms are hierarchical, so more than one GO term per sequence
GUI produces a number of interesting graphs and figures (e.g. hits by organism)

Tested blast2GO commandline b2g4pipe rather than using graphic-interface

accepts only a single xml file
InterPro scan: run independently or within pipeline
Problems with https access. Solved following this guide - looked up data access in blast2GO graphical interface (Tools –> General Settings –> Data Access settings) and updated following section of b2gPipe.properties:

// GO and B2G Data Access Basic Dbacces.dbname=b2g_sep13 Dbacces.dbhost=publicdb.blast2go.com Dbacces.dbuser=blast2go Dbacces.dbpasswd=blast4it