Bambus .mate file

[bye]

Hi,

I'm trying to scaffold velvet output of a de novo assembly of Illumina paired-end data using Bambus. But velvet only output one contigs.fa file, which doesn't contain any pairing information, see below:

>NODE_76_length_102_cov_26.774509
AACTTACCAGGTTCATATCGGATCGAGTTGACCCTTCCGTGAGTCAAAGTATTCCATGCG
CTTCTCAAGCGAAGCTTCAATAAGCTGAGCGTAACTGGGAAGTATGCTTCATCGTTTGTT
TCCAGTGCTT

I can generate .contig file from it, but how can I generate .mate file? Using AMOS tools, I only get one line in .mate file, see below:

library 1 210 390

Which can't generate any scaffolding. Do I need to include original Illumina files that contains short reads as second library to get mate informations?

I'm new to this field and this is my first project. I would really appreciate any help! Thanks a lot in advance!

[Torst]

I'm trying to scaffold velvet output of a de novo assembly of Illumina paired-end data using Bambus. But velvet only output one contigs.fa file, which doesn't contain any pairing information, see below:

FYI - Velvet can do scaffolding for you when you assemble using paired-end reads. You may already be using it without realising it?

[rahularjun86]

Hi,

I'm trying to scaffold velvet output of a de novo assembly of Illumina paired-end data using Bambus. But velvet only output one contigs.fa file, which doesn't contain any pairing information, see below:

>NODE_76_length_102_cov_26.774509
AACTTACCAGGTTCATATCGGATCGAGTTGACCCTTCCGTGAGTCAAAGTATTCCATGCG
CTTCTCAAGCGAAGCTTCAATAAGCTGAGCGTAACTGGGAAGTATGCTTCATCGTTTGTT
TCCAGTGCTT

I can generate .contig file from it, but how can I generate .mate file? Using AMOS tools, I only get one line in .mate file, see below:

library 1 210 390

Which can't generate any scaffolding. Do I need to include original Illumina files that contains short reads as second library to get mate informations?

I'm new to this field and this is my first project. I would really appreciate any help! Thanks a lot in advance!

Hi,
I am also facing the same problem. Did you generate the mate files or not yet. Please share your experience.
cheers,
Rahul

[bye]

Sorry can't help you, I gave up finally. Using CLC workbench instead.