Hello people,
I am using OPERA-LG on bacterial genomic data (more like a test run before I use it on actual mammalian genome) from illumina (short reads) and pacbio (long reads). The short reads were used to generate contigs using velvet. Now when I am executing the OPERA-long-read.pl script on my data, the shorts reads shows zero mapping to the contigs and hence the pipeline is not going forward :( ....Has anyone faced this problem ??? After digging a little deep I found that this following command does the mapping in preprocess.pl : ${path}bowtie -v 3 -a -m 1 -S -t $fasta -p 15 $folder$contigName[ -1 ] - 2>${folder}bowtie.err | sort -n > $folder$outputFile ....can anyone locate what can be the issue ??? any suggestion or help is highly appreciated
