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Closed

Sequence Assembler : PaDeNA always returns contigs even if it runs by enabling Scaffold generation checkBox.

description

PaDeNA always returns contigs even if it runs by clicking Scaffold generation checkBox.
It doesn't return scaffold sequences. Should return scaffold sequence.
Repro steps,
 
1.       Open sequence assembler
2.       Load sequence reads.
3.       Click on Assemble button, select PaDeNA.
4.       Check Scaffold Generation checkbox.
5.       Assemble sequence
(Run PaDeNA for the reads attached in this bug with parameters
Kmer :6,DanglingThreshold:3,RedundantThreshold -7,Redundancy :1,Depth -3.
 
Actual result : PaDeNA returns Contigs not scaffolds.
PaDeNa returns following contigs if  it runs with or without enabling scaffold generation checkBox for the attached file
GCGCGC
TAGCGCGCTA
AGCGCGC
GCGCGCCGCGCG
 Expected result : PaDeNA should return proper scffold sequences if it runs by enabling Scaffold generation checkbox.

file attachments

Closed Aug 10, 2010 at 10:56 AM by ShankarH

comments

wrote Jun 29, 2010 at 9:06 AM

PaDeNA always returns contigs even if it runs by enabling Scaffold generation checkBox.

wrote Jun 29, 2010 at 9:09 AM

wrote Jun 29, 2010 at 4:04 PM

After conversing with the dev team this morning, the ramifications of fixing this bug are large.  Additional parameters would need to be exposed in the dialog, and multiple new and modified test cases would result.  I recommend we move this bug to V2.

wrote Jun 29, 2010 at 4:25 PM

Scaffold step require clone library information input from user depending on the clone library used for sequencing the reads. We currently have 5 libraries as default in framework, but if user uses some other library, then information need to be passed as input.
The library information is required to calculate distance between contigs. This require changes in sequence assembly dialogue box for PaDeNA to get additional parameters.

wrote Jun 29, 2010 at 6:21 PM

We need to spend some time reviewing how the Scaffolding feature is exposed and implemented in the Sequence Assembler.  We will address this in V2, and provide a post-release errata explaining the issue that the Scaffold check box is inop in the Sequence Assembler.

wrote Jul 16, 2010 at 7:50 PM

wrote Aug 6, 2010 at 11:40 AM

Added clone library information text box.

wrote Aug 10, 2010 at 10:56 AM

Verified and regressed in latest build. This issue was fixed. Hence closing this issue.

wrote Nov 3, 2010 at 7:12 PM

leonardoBio wrote Sep 30, 2011 at 4:54 AM

i'm starting to using PaDeNA in cluster in windows HPC 2008, any ideas?

abhisheks wrote Oct 4, 2011 at 12:38 PM

Hi LeonardoBio,

You can use PaDeNa on the HPCS 2008.

We need more specific information about your requirements. This will helps us to answer your query better regarding the use of PaDeNa on the HPCS 2008. Can you please update us on the same.

Regards,
MSR ER Support Team

wrote Feb 13, 2013 at 8:43 PM

wrote May 16, 2013 at 3:16 AM