input files for IMAGE

[Maegwin]

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]

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]

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]

Originally Posted by KanyeDidIt

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]

Originally Posted by gridbird

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.