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General Category >> Bugs and Issues >> new sanger read mapping not producing alignments
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Message started by dlepp on Oct 26th, 2017 at 12:53am

Title: new sanger read mapping not producing alignments
Post by dlepp on Oct 26th, 2017 at 12:53am
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?

Title: Re: new sanger read mapping not producing alignments
Post by Olga Golosova on Oct 26th, 2017 at 12:35pm
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?

Title: Re: new sanger read mapping not producing alignments
Post by dlepp on Oct 26th, 2017 at 9:04pm
Can you tell me which email I can send too?

Thanks

Title: Re: new sanger read mapping not producing alignments
Post by Olga Golosova on Oct 26th, 2017 at 9:25pm
Please send them to ugene@unipro.ru.

Title: Re: new sanger read mapping not producing alignments
Post by Olga Golosova on Oct 27th, 2017 at 11:25pm
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.

Title: Re: new sanger read mapping not producing alignments
Post by dlepp on Nov 2nd, 2017 at 7:02pm
Thanks it is working now.  Like the new viewer, nice that it shows orientation of the mapped read.

Title: Re: new sanger read mapping not producing alignments
Post by Olga Golosova on Nov 2nd, 2017 at 7:09pm
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.

Title: Re: new sanger read mapping not producing alignments
Post by dlepp on Nov 3rd, 2017 at 1:46am
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!

Title: Re: new sanger read mapping not producing alignments
Post by Olga Golosova on Nov 3rd, 2017 at 1:35pm
Thanks! We'll look into this as well. We'll inform you about the result in the nearest future.

Title: Re: new sanger read mapping not producing alignments
Post by Olga Golosova on Nov 7th, 2017 at 4:33pm
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.

Title: Re: new sanger read mapping not producing alignments
Post by Olga Golosova on Nov 23rd, 2017 at 2:40pm
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.

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