Question: OPERA-LG error: short reads are not mapping
0
gravatar for SJ Basu
3.1 years ago by
SJ Basu30
India
SJ Basu30 wrote:

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

scaffolding opera-lg assembly • 1.1k views
ADD COMMENTlink written 3.1 years ago by SJ Basu30
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1807 users visited in the last hour