SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Going from FASTA scaffolds and FASTQ reads to AMOS BANK glacerda Bioinformatics 1 10-04-2011 12:05 AM
AMOS: problem getting hawkeye to view bambus output Kennels Bioinformatics 3 08-24-2011 07:49 PM
convert blast output rururara Bioinformatics 1 04-08-2011 12:48 AM
Editing assembly output of amos? dalesan Bioinformatics 0 04-05-2011 01:59 AM
amos bank-transact show err bah Bioinformatics 4 02-24-2011 11:46 AM

Reply
 
Thread Tools
Old 07-14-2008, 06:34 AM   #1
tjahns
Junior Member
 
Location: Hamburg, Germany

Join Date: Jul 2008
Posts: 9
Default Convert euler-sr output to amos-bank

I'm contemplating using the amos validator to get an impression how useful the euler-sr output really is. But I don't see any obvious way to get the mapping of reads to the generated contig.

Does anyone here know euler-sr or amos well? I'm sort of stuck because if said mapping is not available I don't think I can construct a usable amos-bank.

Thanks for any pointers I might have missed.
tjahns is offline   Reply With Quote
Old 07-20-2008, 10:23 AM   #2
mchaisso
Member
 
Location: Seattle, WA

Join Date: Apr 2008
Posts: 84
Default euler-sr -> amos

If you post a link of what sort of format you want to see, I'll see if I can output that along with an assembly (and supply a converter for finished assemblies).

-mark
mchaisso is offline   Reply With Quote
Old 07-20-2008, 10:26 AM   #3
mchaisso
Member
 
Location: Seattle, WA

Join Date: Apr 2008
Posts: 84
Default

also, let me know what you mean by useful-- it will have impact on some development I do over the next couple of weeks.
mchaisso is offline   Reply With Quote
Old 07-20-2008, 11:37 PM   #4
tjahns
Junior Member
 
Location: Hamburg, Germany

Join Date: Jul 2008
Posts: 9
Default Format for using Amos tools

The best format would probably be an amos/celera assembler message file. You might want to have a look at what velvet does (which can produce such and .afg-file) in this respect.
tjahns is offline   Reply With Quote
Old 07-20-2008, 11:39 PM   #5
tjahns
Junior Member
 
Location: Hamburg, Germany

Join Date: Jul 2008
Posts: 9
Default

Oh and useful refers to using the amosvalidate tool for validation without a reference.
tjahns 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 07:00 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO