IMAGE2 input and parameters

[suryasaha]

I am able to run IMAGE2 after creating read.placed.original and contigs.fa.original in the required format. Here are my questions:
* Is it possible to supply multiple insert libraries to IMAGE? If yes, how?
* What is the difference between "insert size" and "velvet ins_len" in submit.iteration_.log?
* I am working with a bacterial genome. So I assume that all contigs will go into Supercontig1 in read.placed.original. Is that correct?

Please let me know if any question is unclear. Is there a IMAGE mailing list? I was not able to find one on the sourceforge project page. Thanks

-Surya

[suryasaha]

Here is what I learned from the authors
* Is it possible to supply multiple insert libraries to IMAGE? If yes, how?
No
* What is the difference between "insert size" and "velvet ins_len" in submit.iteration_.log?
insert size is the mapping parameter used in ssaha or bwa. velvet ins_len is the insert size used in velvet.
* I am working with a bacterial genome. So I assume that all contigs will go into Supercontig1 in read.placed.original. Is that correct?
Yes

-Surya

[dolphing]

good job~thx

[maasha]

I am looking for some more info on "insert size" and "velvet ins_len". It is not clear which is used for what?

My additional Illumina data have a insert size of 260.

I can set "velvet ins_len" as a parameter to 000_walk_all_raw.pl, but where is "insert size" set?

(IMAGE2 would benefit from a bit more documentation).


Cheers


Martin