########################################## README FILE FOR D.SIMULANS M252 ANNOTATION ########################################## Nicola Palmieri - Institut für Populationsgenetik - Vetmeduni Vienna nicola.palmieri@vetmeduni.ac.at 1. Install the following software from the reported links: * BEDTools 2.17.0: https://code.google.com/p/bedtools/ * BLAT: https://genome.ucsc.edu/FAQ/FAQblat.html#blat3 * Cufflinks 2.0.2: http://cufflinks.cbcb.umd.edu/ * Exonerate 2.2.0: http://www.ebi.ac.uk/~guy/exonerate/ * Picard 1.87: http://picard.sourceforge.net/ * SAMtools 0.1.19: http://samtools.sourceforge.net/ * TopHat 2.0.8: http://ccb.jhu.edu/software/tophat/index.shtml * Trinity (2013-02-25): http://trinityrnaseq.sourceforge.net/ 2. Add all the executables to the PATH except for Picard and Trinity. 3. Download RNA-Seq reads in FASTQ format from the NCBI Sequence Read Archive (SRA) using accession ID SRR1212716. Rename the read files as BGI_26a_120211_I248_FCD0KN9ACXX_L8_CSZPE0120107166_1.fq and BGI_26a_120211_I248_FCD0KN9ACXX_L8_CSZPE0120107166_2.fq and put them into the folder 1-reads. 4. Run step-by-step the Dsim-M252-annotation.sh for annotation of the assembly located at 2-assembly/dsim-all-chromosome-M252_draft_4-chrnamesok.fa. The output file will be located in 3-annotation/dsim-M252-popgen-ann-r1.0.gtf and it will contain annotation for exons, introns, CDSs and UTRs.