Opera Scaffolding Error: Reads In The Wrong Orientation
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10.7 years ago
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Hi everyone I am using Opera for Scaffolding with mapping tool bwa . I am getting an error : Please help me out

I am using like this

perl preprocess_reads.pl contigsH10.fasta ResetH10_S1_L001_R1_001.fastq ResetH10_S1_L001_R2_001.fastq lib_1.map bwa
------------------------------------------------
[main] Version: 0.6.1-r104
[main] CMD: bwa samse -n 1 contigsH10.fasta read.sai -
[main] Real time: 14.802 sec; CPU: 14.149 sec
[Fri Sep  6 12:45:56 2013]    Preprocessing done!

./opera contigsH10.fasta lib_1.map outH10

Step 1: Setting parameters ...
Time Taken: 0.000135 seconds
Step 2: Reading contig file ...
Time Taken: 0.012631 seconds
Step 3: Reading mapping file ...
The orientation of reads is not "in", "out", neither "forward", Opera could not handle such orientation. Please check the mapping files. Please feel free to contact gaosong@nus.edu.sg for further support. 
ERROR: Converting mapping file error!
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10.7 years ago

Opera is a "Optimal Paired-End Read Assembler" but you used the single-end mapper of bwa (samse)

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I am using like this in command line

$ perl bin/preprocess_reads.pl test_dataset/contigs_H10.fasta test_dataset/ResetH10_S1_L001_R1_001.fastq.gz test_dataset/ResetH10_S1_L001_R2_001.fastq.gz test_dataset/lib_1.bam bwa

Next :

$ bin/opera test_dataset/contigs_H10.fasta test_dataset/lib_1.bam,test_dataset/lib_2.bam test_dataset/results2

Could you please have a look the command ?

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