SeqMan NGen Product Notifications

SeqMan NGen

DNASTAR no longer supports SeqMan NGen on Linux

Date: 3/2/17

 

Version Affected: 14.1 and later

 

Version Fixed: N/A

 

Issue: As of March 2, 2017, corresponding with the release of Lasergene 14.1, DNASTAR no longer supports SeqMan NGen for the Linux operating system. We will continue to support SeqMan NGen for Windows and Macintosh.

 

Resolution: If you have questions about this change, please contact DNASTAR at 866-511-5090 or sales@dnastar.com.

Issues with RNA-Seq or ChIP-Seq workflows on non-English Windows systems

Date: 6/12/17

 

Version Affected: 14.1 and earlier

 

Version Fixed: 14.1.2

 

Issue: Users running Windows machines with an active non-English language pack or with certain non-American region settings may experience issues (e.g. stalling or errors during assembly), particularly with RNA-Seq or ChIP-Seq workflows in SeqMan NGen.  These issues are partially related to the software not recognizing certain regional number settings: where characters other than a comma are used to separate groups of digits, or where characters other than a period are used for the decimal symbol.

 

Resolution: This issue has been addressed in the 14.1.2 patch released June 12, 2017. To avoid or correct this issue, please upgrade to the current version of Lasergene. For assistance, contact DNASTAR at 866-511-5090 or sales@dnastar.com.

Note regarding Variant Annotation Databases based on GRCh37 and GRCh38

Date: 5/5/2017

 

Version Affected: 13.1 to 14.1

 

Version Fixed: NA

 

Issue: The Variant Annotation Database (VAD) based on human genome reference GRCh37 was first released with Lasergene 13.1 in March 2016. With the March 2017 release of  Lasergene 14.1,  a companion VAD version was added, based on human genome reference GRCh38. DNASTAR software automatically detects which version of the human genome reference sequence is used in a SeqMan NGen assembly and accesses the corresponding VAD for variant annotation.

 

The aforementioned Lasergene 14.1 release also included an update of the GRCh37 version of the VAD and the removal of Polyphen2 data from both VAD versions due to licensing issues.

 

In  May 2017, to address some data inconsistencies caused by changes in the reference sequence between the GRCh37 and GRCh38 VAD builds, the GRCh37 version was reverted to its pre-Lasergene 14.1 state. We also anticipate some cases in which annotations from the GRCh38 version of the VAD will be missing, due to the changes in the reference sequence.

 

Resolution: DNASTAR will continue to update the VAD periodically and will strive to address any remaining inconsistencies between the two versions.  In the interim, there may be cases where the data and annotations do not align as expected. For questions regarding this topic, please contact DNASTAR at 866-511-5090 or sales@dnastar.com.

Targeted aligned reads are not properly reported

Date: 4/26/16

 

Version Affected: 13.0.0 

 

Version Fixed: 13.0.1/13.02 included in Lasergene 13.0c installer

 

Issue: In SeqMan NGen version 13.0.0, the number of targeted aligned reads is not properly reported due to an issue handling duplicate reads. This issue can be seen in the Enrichment Report section of the Coverage of Target Regions Report in SeqMan Pro.

 

Resolution: To address this issue, log in to your DNASTAR account and update your SeqMan NGen software to version 13.0.1, which is included in the Lasergene 13.0c installer. Please contact DNASTAR at 866-511-5090 or sales@dnastar.com if you need assistance.

When using SeqMan NGen’s Viral-Host Integration workflow, unexpectedly few reads align to the host genome

Date: 4/7/16

 

Version Affected: 13.0

 

Version Fixed: 13.0.1

 

Issue: In SeqMan NGen v. 13.0, the Viral-Host Integration workflow may lead to an unexpectedly low number of reads aligning to the host genome. This issue has been addressed with the release of a patch, Lasergene v. 13.0.1.

 

Resolution: To address this issue, log in to your DNASTAR account and update your Lasergene software to version 13.0.1. Please contact DNASTAR at 866-511-5090 or sales@dnastar.com if you need assistance.

When using SeqMan NGen’s transcript annotation workflow, few identified transcripts are reported

Date: 4/7/16

 

Version Affected: 13.0

 

Version Fixed: 13.0.1

 

Issue: Due to a non-optimal background parameter setting in SeqMan NGen v. 13.0, the transcript annotation workflow may produce an unexpectedly low number of identified transcripts. This issue only affects the transcript annotation (de novo Transcriptome/RNA-Seq) workflow. This issue has been addressed with the release of a patch, Lasergene v. 13.0.1.

 

Resolution: To address this issue, log in to your DNASTAR account and update your Lasergene software to version 13.0.1. Please contact DNASTAR at 866-511-5090 or sales@dnastar.com if you need assistance.

SeqMan NGen no longer detects quality scores in pre-2011 Illumina data by default

Date: 3/1/16

 

Version Affected: 12.3 and earlier

 

Version Fixed: N/A

 

Issue: As of the Lasergene 13.0 release, SeqMan NGen will no longer detect quality scores in pre-2012 Illumina data by default.

 

Resolution: Starting with the Lasergene 13.0 release (March 2016), SeqMan NGen uses a standard offset for Illumina data rather than basing the offset on Illumina quality scores. If you are using pre-2012 Illumina data, you can direct SeqMan NGen to detect quality scores for those data by following these steps:

 

  1. Set up the SeqMan NGen project as desired. When you reach the Assembly Output screen, press the Save Script button. Then press the Quit button to exit from SeqMan NGen.
  2. Open the saved script in a text editor. Replace any occurrences of the words “Illumina” or “IlluminaLongReads” with either “auto” or “IlluminaQual64.” Both replacements are interchangeable. Save the edited script.
  3. Use the edited script to perform a SeqMan NGen assembly. To do this, open the Command Prompt (Win) or Terminal (Mac). Type: XNG [filepath\script name] and press Enter.

 

Please contact DNASTAR at 866-511-5090 or sales@dnastar.com for assistance.

Macintosh OS X 10.11 “El Capitan” is not compatible with Lasergene version 12.3.1 or earlier

Date: 10/13/15

 

Version Affected: 12.3.1 and earlier

 

Version Fixed: 12.3.2

 

Issue:  Macintosh released operating system OS X 10.11 “El Capitan” on 9/30/15. This operating system is incompatible with Lasergene version 12.3.1 or earlier. If you have Lasergene version 12.3.1 or earlier, updating to El Capitan will cause the loss of important Lasergene functionality, including the ability to:

 

  • Open, close and save files.
  • Run applications through the command-line (SeqMan NGen, SeqNinja).

 

Resolution: This issue is fixed in Lasergene 12.3.2, released on 10/13/15. If you download and install this version of Lasergene (or later), you may update your Macintosh system to “El Capitan” while retaining full Lasergene functionality.

 

Please contact DNASTAR at 866-511-5090 or sales@dnastar.com for information on upgrading your applications to the latest versions.

 

 

A warning message that the “identity of the developer cannot be confirmed” appears when attempting installation of DNASTAR software on Macintosh OS X 10.9.5 and later

Date: 9/18/2014

 

Version Affected: 12.0 and 12.0.1

 

Version Fixed: 12.1

 

Issue: Macintosh OS X 10.9 (Mavericks) and later require a “v2” signature. Lasergene 12.0 and 12.0.1 have a “v1” signature. Therefore, when attempting to install Lasergene 12.0 or 12.0.1 or its components on Macintosh OS X 10.9.5 (or later), the following message appears: “[ApplicationName] 12.x.x Mac Install can’t be opened because the identity of the developer cannot be confirmed.”

 

Resolution:

 

To correct this issue:

 

After the release of Lasergene 12.1, please log in and download the most recent version of the software. If you need assistance, contact DNASTAR at 866-511-5090 or support@dnastar.com for help.

 

Prior to the release of Lasergene 12.1, or if you do not wish to upgrade to that version, you may circumvent the issue as follows:

 

  1. Click the OK button to close the warning.
  2. Ctrl+click on the file named [ApplicationName] 12.x.x Mac Install and select Open. You will see a warning that appears similar to the original warning.
  3. Click the Open button at the bottom of the new message.

 

The installer will now run as normal.

 

Templated assembly fails when using certain reference sequences or genome templates

Date:   7/28/2014

 

Version Affected:  12.0 and earlier

 

Version Fixed:  12.0.1

 

Issue:  Rarely, specific reference sequences or genome templates may cause SeqMan NGen to crash during the assembly phase.

 

Resolution:   Crashes have been reported to occur when using particular GenBank (*.gbk) or General Feature Format (*.gff) files, and for the Arabidopsis 138 template. However, it may also occur for other file types or genome templates.

 

This issue was fixed in 12.0.1. If you are experiencing this problem, please request a download link by contacting DNASTAR Support at 866-511-5090 or support@dnastar.com.

 

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