Welcome, Guest. Please Login or Register
UGENE Bulletin Board
  Welcome to our forum.
  HomeHelpSearchLoginRegister  
 
 
Page Index Toggle Pages: 1
new sanger read mapping not producing alignments (Read 502 times)
Oct 26th, 2017 at 12:53am

dlepp   Offline
YaBB Newbies

Posts: 8
*
 
In the past I have used the Sanger data analysis tool to check sequencing results, but I find the new version "Map reads to reference.." gives an error "Subtask {Compose alignment} is failed: No read satisfy minimum identity criteria." even for reads that aligned in the past, or have 97% identity when aligned with blastn.  Any idea what could be the problem?
 
IP Logged
 
Reply #1 - Oct 26th, 2017 at 12:35pm

Olga Golosova   Offline
YaBB Administrator

Posts: 211
*****
 
Hi! We're sorry for your bad experience! And we would be very grateful, if you send us the data (e.g. by e-mail), so we can reproduce the issue locally.

Meanwhile, would you like me to give you a link to the previous UGENE version? Do you use Windows OS?
 
IP Logged
 
Reply #2 - Oct 26th, 2017 at 9:04pm

dlepp   Offline
YaBB Newbies

Posts: 8
*
 
Can you tell me which email I can send too?

Thanks
 
IP Logged
 
Reply #3 - Oct 26th, 2017 at 9:25pm

Olga Golosova   Offline
YaBB Administrator

Posts: 211
*****
 
Please send them to ugene@unipro.ru.
 
IP Logged
 
Reply #4 - Oct 27th, 2017 at 11:25pm

Olga Golosova   Offline
YaBB Administrator

Posts: 211
*****
 
Thanks for the data!
Note that we updated the algorithm for mapping Sanger reads in UGENE 1.28. We've checked it with the data you sent and the read has been mapped successfully.

The new version 1.28 will be released at the beginning of the next week. We appreciate if you check the new algorithm and inform us, if everything is fine.
 
IP Logged
 
Reply #5 - Nov 2nd, 2017 at 7:02pm

dlepp   Offline
YaBB Newbies

Posts: 8
*
 
Thanks it is working now.  Like the new viewer, nice that it shows orientation of the mapped read.
 
IP Logged
 
Reply #6 - Nov 2nd, 2017 at 7:09pm

Olga Golosova   Offline
YaBB Administrator

Posts: 211
*****
 
Thanks for informing and sharing with us your opinion about the viewer.
If you have any additions to your feedback in future, you're also welcome to share it.
 
IP Logged
 
Reply #7 - Nov 3rd, 2017 at 1:46am

dlepp   Offline
YaBB Newbies

Posts: 8
*
 
I may have spoken too soon - while some reads are now aligning properly, others that align well via online blastn still do not map using ugene.  I have sent test data in another email.

Thanks!
 
IP Logged
 
Reply #8 - Nov 3rd, 2017 at 1:35pm

Olga Golosova   Offline
YaBB Administrator

Posts: 211
*****
 
Thanks! We'll look into this as well. We'll inform you about the result in the nearest future.
 
IP Logged
 
Reply #9 - Nov 7th, 2017 at 4:33pm

Olga Golosova   Offline
YaBB Administrator

Posts: 211
*****
 
Hello again!

Please note that "Mapping min quality" parameter in the "Map Sanger Reads to Reference" has another meaning than the "Identity" value of a BLAST pairwise alignment:
* The first one specifies identity between the whole read and the corresponding region of the reference sequence.
* The second one specified identity between the aligned part of the read and the corresponding region of the reference sequence.

However, we found out that there were indeed a bug in the filtering by identity. See UGENE-5863 for details.

Thank you again for the report and the data. The issue will be fixed in UGENE 1.28.1 that will come out soon.
 
IP Logged
 
Reply #10 - Nov 23rd, 2017 at 2:40pm

Olga Golosova   Offline
YaBB Administrator

Posts: 211
*****
 
UGENE 1.28.1 has been released recently. The issue is fixed.

Note that the "Identity" parameter in the dialog was replaced by "Silmilarity" as the mapping algorithm takes into account gaps when comparing reference and read. See the "Mapping Reads to Reference" chapter in the documentation for details.

Your feedback about the new UGENE version is welcome.
 
IP Logged
 
Page Index Toggle Pages: 1