CAP3 output *.ace in EagleView?

mucku · 01-21-2009, 01:44 PM

Hello,
I am a molecular biologist. We have done some EST sequencing and I used TGICL / CAP3 for sequence assembly. Everything works fine and it constructs all the contigs etc. Now I wanted to check the *.ace output visually in EagleView. I get an error stating:

"Error: BS missing or in an wrong order!"

I checked the *.ace file and there is no information in corresponding to a "BS" tag. But anyways... After reading the documentation of EagleView this data shouldn't be needed anyway:
"EagleView extracts information defined in the seven tags: AS CO BQ AF RD QA DS, and skip all other information."

I looked around and found a sort of minimal info ACE viewer: BEAP

http://www.animalgenome.org/bioinfo/...userguide.html

This one is displaying my contigs. I can see overlaps of the subsequences etc... But only as crappy bars with no extra info whatsoever...

Am I just using the wrong software for what I am trying to see? Is EagleView not capable of displaying data without the BS tag?

I worked myself into Linux 3 months ago and am capable of using programs like TGICL and others.

But I can't program any scripts for extracting data or so...

Any help would be appreciated!

montera · 10-26-2009, 10:16 AM

Hi,
I'm trying to get CAP3, but the server is out! Do you have the executable? Can you provide it to me?
thanks a lot

mucku · 10-26-2009, 01:13 PM

Hello,
CAP3 is also part of the TGICL package. So you can just download it and use CAP3 from it. For which operating system do you need it for? It's also available as a Biolinux package.

http://compbio.dfci.harvard.edu/tgi/software/

I hope this helped you.

Mucku

saurabh_r · 10-27-2009, 12:30 AM

Hi,
Just wondering, why not use CONSED (www.phrap.org) to view and edit the .ace file.

SR

sklages · 10-27-2009, 12:47 AM

EagleView is probably a bad choice for viewing EST assemblies. Consed might be better. You also might want to test clview (from the same TGICL site) for viewing your assembled clusters.

In general, I'd recommend MIRA3 (http://chevreux.org/projects_mira.html) for assembly of sanger/454 based EST datasets. It works fine (at least in my hands) and lets you the choice using ACE based viewers, Staden's gap4/gap5 or even nedit ;-)

hth,
Sven

colindaven · 10-27-2009, 01:10 AM

That s interesting. I had the exact same BS problem with an ace file supplied to us by a sequencing company.

No solution yet I'm afraid!

Consed also came up with the following error:

There are not enough BaseQuality values for all non-pad consensus bases for contig

Colin

sklages · 10-27-2009, 01:29 AM

Consed uses all tags in the ace file and is therefore most sensitive to errors.
What kind of ACE file have you been given? How was it assembled?

Sven

mucku · 10-27-2009, 01:35 AM

That's funny... my question is like 9 months old. Then "montera" asked for CAP3 and suddenly the answers are popping up. Well I will try CONSED although I don't need this anymore at this moment.

Thx
Better late than never... :-)

sklages · 10-27-2009, 01:39 AM

That's really funny. I just had a look at "montera"'s date and your post. Nevertheless, maybe someone else stumbles over this kind of problem :-)

bis denne,
Sven

montera · 10-27-2009, 04:27 AM

Thanks everyone. I have already asked for consed (but it can take 2 weeks)... But about CAP3, nobody used it?

mucku · 10-27-2009, 04:50 AM

I thought i sent you a message montera.
CAP3 is also part of the TGICL package (http://compbio.dfci.harvard.edu/tgi/software/). Just download TGICL and you will have CAP3 too.

mucku · 10-27-2009, 04:53 AM

Hi. I thought I already did send you a private message montera. CAP3 is also included in the TGICL package (http://compbio.dfci.harvard.edu/tgi/software/). Just download TGICL and you will have CAP3.

Greetings

kmcarr · 10-27-2009, 05:41 AM

Quote:

Originally Posted by montera

Thanks everyone. I have already asked for consed (but it can take 2 weeks)... But about CAP3, nobody used it?

Montera, many people use CAP3 but the license does not allow users to redistribute the software. You have to agree to the license terms and then the author will make the software available to you. As the web site is currently down you might try contacting the author directly: xqhuang@cs.iastate.edu.

montera · 10-27-2009, 06:24 AM

Okay, understand.... I wrote to xqhuang@cs.iastate.edu and I'm still waiting... Thanks

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01-21-2009, 01:44 PM	#1
mucku Member Location: Berlin Join Date: Jan 2009 Posts: 14	*CAP3 output .ace in EagleView?** Hello, I am a molecular biologist. We have done some EST sequencing and I used TGICL / CAP3 for sequence assembly. Everything works fine and it constructs all the contigs etc. Now I wanted to check the .ace output visually in EagleView. I get an error stating: "Error: BS missing or in an wrong order!" I checked the .ace file and there is no information in corresponding to a "BS" tag. But anyways... After reading the documentation of EagleView this data shouldn't be needed anyway: "EagleView extracts information defined in the seven tags: AS CO BQ AF RD QA DS, and skip all other information." I looked around and found a sort of minimal info ACE viewer: BEAP http://www.animalgenome.org/bioinfo/...userguide.html This one is displaying my contigs. I can see overlaps of the subsequences etc... But only as crappy bars with no extra info whatsoever... Am I just using the wrong software for what I am trying to see? Is EagleView not capable of displaying data without the BS tag? I worked myself into Linux 3 months ago and am capable of using programs like TGICL and others. But I can't program any scripts for extracting data or so... Any help would be appreciated!

10-27-2009, 12:30 AM	#4
saurabh_r Junior Member Location: India Join Date: Oct 2009 Posts: 2	Consed Hi, Just wondering, why not use CONSED (www.phrap.org) to view and edit the .ace file. SR

10-26-2009, 10:16 AM	#2
montera Junior Member Location: brasil Join Date: Jul 2009 Posts: 5	Hi, I'm trying to get CAP3, but the server is out! Do you have the executable? Can you provide it to me? thanks a lot

10-26-2009, 01:13 PM	#3
mucku Member Location: Berlin Join Date: Jan 2009 Posts: 14	Hello, CAP3 is also part of the TGICL package. So you can just download it and use CAP3 from it. For which operating system do you need it for? It's also available as a Biolinux package. http://compbio.dfci.harvard.edu/tgi/software/ I hope this helped you. Mucku

10-27-2009, 12:47 AM	#5
sklages Senior Member Location: Berlin, DE Join Date: May 2008 Posts: 628	EagleView is probably a bad choice for viewing EST assemblies. Consed might be better. You also might want to test clview (from the same TGICL site) for viewing your assembled clusters. In general, I'd recommend MIRA3 (http://chevreux.org/projects_mira.html) for assembly of sanger/454 based EST datasets. It works fine (at least in my hands) and lets you the choice using ACE based viewers, Staden's gap4/gap5 or even nedit ;-) hth, Sven

10-27-2009, 01:10 AM	#6
colindaven Senior Member Location: Germany Join Date: Oct 2008 Posts: 415	That s interesting. I had the exact same BS problem with an ace file supplied to us by a sequencing company. No solution yet I'm afraid! Consed also came up with the following error: There are not enough BaseQuality values for all non-pad consensus bases for contig Colin

10-27-2009, 01:29 AM	#7
sklages Senior Member Location: Berlin, DE Join Date: May 2008 Posts: 628	Consed uses all tags in the ace file and is therefore most sensitive to errors. What kind of ACE file have you been given? How was it assembled? Sven

10-27-2009, 01:35 AM	#8
mucku Member Location: Berlin Join Date: Jan 2009 Posts: 14	That's funny... my question is like 9 months old. Then "montera" asked for CAP3 and suddenly the answers are popping up. Well I will try CONSED although I don't need this anymore at this moment. Thx Better late than never... :-)

10-27-2009, 01:39 AM	#9
sklages Senior Member Location: Berlin, DE Join Date: May 2008 Posts: 628	That's really funny. I just had a look at "montera"'s date and your post. Nevertheless, maybe someone else stumbles over this kind of problem :-) bis denne, Sven

10-27-2009, 04:27 AM	#10
montera Junior Member Location: brasil Join Date: Jul 2009 Posts: 5	Thanks everyone. I have already asked for consed (but it can take 2 weeks)... But about CAP3, nobody used it?

10-27-2009, 04:50 AM	#11
mucku Member Location: Berlin Join Date: Jan 2009 Posts: 14	I thought i sent you a message montera. CAP3 is also part of the TGICL package (http://compbio.dfci.harvard.edu/tgi/software/). Just download TGICL and you will have CAP3 too.

10-27-2009, 04:53 AM	#12
mucku Member Location: Berlin Join Date: Jan 2009 Posts: 14	Hi. I thought I already did send you a private message montera. CAP3 is also included in the TGICL package (http://compbio.dfci.harvard.edu/tgi/software/). Just download TGICL and you will have CAP3. Greetings

10-27-2009, 06:24 AM	#14
montera Junior Member Location: brasil Join Date: Jul 2009 Posts: 5	Okay, understand.... I wrote to xqhuang@cs.iastate.edu and I'm still waiting... Thanks