Hello everyone,

I am quite new to the program, but tutorials on youtube and topics on this forum were quite helpful to get this far.
So, I have ab1 files with forward and reverse strand (different primers). I managed to get the reverse complement, find the consensus, export it and in final step (just like in this video: "Unipro UGENE podcast #52: The Sanger Reads Editor in UGENE 1.27") I get the following error: ugene Error: Subtask {Compose alignment} is failed: No read satisfy minimum similarity criteria.

Really don't know what am I doing wrong. In the input data I put my consensus file in "reference" tab, and in "reads" I add those two aforementioned ab1 files with different primers. Everything else is by default (Trimming quality threshold 30; Mapping min similarity 80).

Thanks in advance guys
Mateo

Hello Dmitrii,

Thank you so much! After I tried your solution it worked. However, I adjusted "Mapping min similarity" to 0%. Can there be a problem with putting that low of a percentage? In other words, is it more advisable to decrease that parameter by smaller margins (say 10% at a time) and figure out what is the first percentage that would work?

Hello again,
As I've already said, after every "Trim and map Sanger reads" run you've got the notification in the right-bottom corner - blue or red, depends on whether the execution went good or not. You may click on it and the execution report will be opened.  In this report, you may find the information about similarity. Try to check it and you will see, what value you need.

Hello again, sorry for waiting,
There are signs in the log "read_name was skipped. No BLAST results". That means that the BLAST tool, which looks for the approximate place in the sequence, where the read should be put on, couldn't find any region for this read. In general, reads you've tried to align aren't fit to the reference at all.

The idea is that your read and reference are too different to find any way to align them with each other. If you send me your data, I'll take a look at them and, maybe, it'll help me to tell you more information.

You can download them, for example, on google drive and send me a link to the folder.

Yes, I can. I downloaded files and now I can see. The reference sequence and reads aren't looked similar so it's not surprising that mapping doesn't finish well. BLAST just couldn't find a place on the reference where to put the input reads. I think, you need another reference sequence.

Interesting! Thanks for posting.