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-   -   input files for IMAGE (http://seqanswers.com/forums/showthread.php?t=10204)

Maegwin 03-21-2011 04:54 AM

input files for IMAGE
 
Hi everybody,

I'm currently working on the assembly of two bacterial genome sequences from an illumina GAIIx sequencer. I have made a de novo assembly of the 50bp paired end reads with velvet and now would like to try to close some gaps with IMAGE.


In the very short description of IMAGE i found the following necessary input files:
a contigs.fa.original file in FASTA format.
a read.placed.original file containing a list of contigs within supercontigs.
Paired end Illumina fastq files (should be unzipped)


From Velvet I got the contigs.fa file and I have Paired end fastq files, but from which program will I get a read.placed.original file? Or did I miss some options for velvet?

I'm still quite new in the field of bioinformatics and not used to use linux, so could you please explain everything very simple ;)

Thanks,
Maegwin

KanyeDidIt 03-21-2011 07:36 AM

You need to write a simple script with perl to produce a read.placed.original file in the format that comes with the example file.

Maegwin 03-22-2011 12:12 AM

Ok, so actually I never wrote a script, so how to do this?
I will check on some Online-Tutorials on how to write a Pearl Script.

gridbird 04-22-2011 04:32 PM

Quote:

Originally Posted by KanyeDidIt (Post 37615)
You need to write a simple script with perl to produce a read.placed.original file in the format that comes with the example file.

I don't know the corresponding between contigs and scaffold contigs. how do I write script? what is the input of this script?

KanyeDidIt 04-22-2011 04:54 PM

Quote:

Originally Posted by gridbird (Post 40183)
I don't know the corresponding between contigs and scaffold contigs. how do I write script? what is the input of this script?

If the contigs are in Pcap format its kind of easy to indentify the contig - scaffold relationship.

Contig5.1, Contig5.2..... should belong to Scaffold5. Something similar to that. This can be customizable for other formats if you have scaffolding information I guess.


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