Similar protocols

Pipeline publication

[…] sequence of B. ovata with Tophat2. Paired-end reads that failed to be mapped were subtracted by SAMtools. AUGUSTUS in step 1 was performed as follows. An intron hints file with gff format was created by bam2hints script using the Bam file originating from the mapping step. The first AUGUSTUS pass was performed with the trained parameter based on B. bovis, the hints gff file, and a parameter file, extrinsic.M.RM.E.W.cfg, which was bundled in the package. The results and hint gff were integrated to obtain an intron dataset and converted to obtain an exon–exon junction database (exex.fa and map.psl) by intron2exex.100.pl script modified from the original intron2exex.pl to accept 100-bp reads. AUGUSTUS analysis in step 2 was performed as follows. The MiSeq RNAseq reads were mapped to the exon–exon junction database with Bowtie2 to obtain spliced reads and their mapped profiles. Unmapped reads were discarded with SAMtools and then the remaining sequences were formatted with SAMmap.pl script with reference to map.psl. The mapped results of the MiSeq reads on B. ovata were further filtered to remove N nucleotides with BamTools with operation N filter.txt script in the AUGUSTUS package. The filtered and mapped results were merged with those for spliced reads annotated as above. Another intron file, hints 2, was generated from the merged mapped profile and then a second AUGUSTUS implementation was performed with the trained parameter, hints 2, and extrinsic.M.RM.E.W.cfg., Functional annotation of B. ovata genes, including GO terms, was conducted by Blast2GO []. tRNA and rRNA genes in the genome were pred […]

Pipeline specifications

Software tools AUGUSTUS, Bowtie2, SAMtools