Tool:opera scaffolding problem

Question

[Rahul]

Hello,

I am facing some problem while using Opera tool. I have already used Velvet over reads (forward fastq and reverse fastq files) through which I got contigs.fa file. Assuming I have all input files I tried opera but getting error messages. I am also bit confuse about commands to be used for my data. I would be very grateful if anyone could shade some light on my problem.

I have used following commands

e.g.

bin/preprocess_reads.pl test_dataset/contigs.fa test_dataset/reads_1.fa test_dataset/reads_2.fa test_dataset/reads.map

1 command

bin/preprocess_reads.pl test_dataset/contigs.fa test_dataset/ pt10001.fastq test_dataset/pt10002.fastq test_dataset/reads.map

2 command

bin/preprocess_reads.pl test_dataset/contigs.fa test_dataset/ pt10001.fastq test_dataset/pt10002.fastq

Thanks

[nterhoeven]

can you please post the error messages? This would help answering your question