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Old 09-11-2015, 12:52 AM   #1
Jepang-Beriman
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Location: Japan

Join Date: Jan 2015
Posts: 3
Default RAST had my ordered contigs being re-ordered

Greetings,

First of all, please forgive me if my words happen to be totally incomprehensible since I don't have any prior knowledge of bioinformatics.

I would like to ask for advise regarding my research, particularly in using RAST.

I am currently preparing my data for bacterial whole genome comparison. I am following steps as outlined from this paper: http://holtlab.net/2014/12/27/bacter...cs-tutorial-2/, with certain adjustments.

My data source is couple of paired-end reads from Illumina MiSeq of S. aureus. I've had assembled draft contigs by using SPAdes and had the assembled contigs ordered against reference genome by using Mauve contig mover. Later on, I've had the reference-ordered contig being annotated by using web-based RAST.

However, RAST had my annotated contigs being re-ordered, which was entirely in different order compared to the input draft contigs, so I couldn't easily plot the annotation back into my draft contigs.

I've tried to re-order the RAST contigs back into my draft contigs' orientation using Mauve contig mover (after I concatenate my draft contigs into single continuous FASTAs), the RAST contigs were re-ordered well but somehow the metadata of each of these annotations was gone, it only showed blank annotated regions.

I would like to ask for advice on how to overcome this problem; did I missed some details during RAST annotation, or was it there something wrong to my draft contigs?

I need to have my draft contigs ordered against the reference and annotated, so I could make a comparison alignment for these samples (n>50).

Thank you very much for your kind supports.
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