SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Several input files w. Novoalign? kga1978 Bioinformatics 18 11-23-2011 01:57 AM
SVA input files srd Introductions 0 03-16-2011 07:17 AM
IMAGE input files skingan Genomic Resequencing 0 07-29-2010 01:02 PM
BWA - input files Bruins Bioinformatics 2 07-07-2010 12:43 AM
For sequence quality assessment, do the raw image files provide any added value? throwaway SOLiD 9 04-14-2010 08:02 AM

Reply
 
Thread Tools
Old 03-21-2011, 05:54 AM   #1
Maegwin
Junior Member
 
Location: Germany

Join Date: Mar 2011
Posts: 2
Default 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
Maegwin is offline   Reply With Quote
Old 03-21-2011, 08:36 AM   #2
KanyeDidIt
Junior Member
 
Location: US

Join Date: Sep 2010
Posts: 8
Default

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.
KanyeDidIt is offline   Reply With Quote
Old 03-22-2011, 01:12 AM   #3
Maegwin
Junior Member
 
Location: Germany

Join Date: Mar 2011
Posts: 2
Default

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.
Maegwin is offline   Reply With Quote
Old 04-22-2011, 05:32 PM   #4
gridbird
Member
 
Location: san diego

Join Date: Oct 2010
Posts: 16
Default

Quote:
Originally Posted by KanyeDidIt View Post
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?
gridbird is offline   Reply With Quote
Old 04-22-2011, 05:54 PM   #5
KanyeDidIt
Junior Member
 
Location: US

Join Date: Sep 2010
Posts: 8
Default

Quote:
Originally Posted by gridbird View Post
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.
KanyeDidIt is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 06:42 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO