Question: Using idba_un to read xxx.fa output into xxx_dir file, terminator showed invalid insert distance
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gravatar for wuziqi_94
3.1 years ago by
wuziqi_940
wuziqi_940 wrote:

When I do the assembly, after merge xxx_1.fp and xxx_2.fp files into xxx_1.fa file, I used idba_un to read xxx_1.fa output into xxx_dir. One the screen, the terminator showed the invalid insert distance which was following the kmer command line. How to fix this problem? And what is the problems with invalid insert distance?

assembly • 1.1k views
ADD COMMENTlink modified 2.6 years ago by Biostar ♦♦ 20 • written 3.1 years ago by wuziqi_940

Are you sure that the reads are properly paired and follows the same order in both fastq files prior to merging as that can cause such error in idba.

ADD REPLYlink written 3.1 years ago by Sej Modha4.7k

Thank you! I am sure that both two reads are properly paired and follow the same order in both fastq files. I am confused about how to fix the insert distance in IDBA to assembly the fastq files.

ADD REPLYlink written 3.1 years ago by wuziqi_940
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