opened
mpoelchau
username_0
Hi y'all,

I noticed this on our current instance of WA1.0.4 and was able to replicate the issue on the WA2 demo on icebox. If you drag and drop evidence into the Uca track (I've tried RNA-Seq reads and mRNA so far) and flip the strand, models are 1) not truncated at the first stop codon in either the display or the gff3, and 2) the protein sequence is truncated, but not always at the first stop codon. I've created some examples of this on the icebox WA2 site for Honey1 at Group1.1:963667..963843 (177 b). It seems that the gff3 and display coordinates are calculated from the original strand. 

![screen shot 2015-07-08 at 1 59 06 pm 2](https://cloud.githubusercontent.com/assets/5487172/8580747/86eda4c0-2579-11e5-8875-10aa19f8bd66.png)


Issue may or may not be related to issue #55. 

Also, from looking at the protein sequences calculated from these models, I have to admit that I'm confused as to how WA2 determines whether a TGA should represent a selenocysteine or a stop codon in the calculated protein sequence. I look forward to reading the documentation on this later on!
'Move to Opposite Strand' function does not recognize stop codons in display or gff3
issue
created
nathandunn
username_1
Ack.  I will take a look.  Glad you found it in both as I used the smart code in both.
comment
created
deepakunni3
username_2
@username_1 The fact that the transcript, once flipped to the opposite strand, doesn't have the proper CDS is because setLongestORF() method is not being called.
comment
closed
deepakunni3
username_2
issue
created
nathandunn
username_1
Still need to have @username_3  and @username_0  check this.
comment
reopened
nathandunn
username_1
Hi y'all,

I noticed this on our current instance of WA1.0.4 and was able to replicate the issue on the WA2 demo on icebox. If you drag and drop evidence into the Uca track (I've tried RNA-Seq reads and mRNA so far) and flip the strand, models are 1) not truncated at the first stop codon in either the display or the gff3, and 2) the protein sequence is truncated, but not always at the first stop codon. I've created some examples of this on the icebox WA2 site for Honey1 at Group1.1:963667..963843 (177 b). It seems that the gff3 and display coordinates are calculated from the original strand. 

![screen shot 2015-07-08 at 1 59 06 pm 2](https://cloud.githubusercontent.com/assets/5487172/8580747/86eda4c0-2579-11e5-8875-10aa19f8bd66.png)


Issue may or may not be related to issue #55. 

Also, from looking at the protein sequences calculated from these models, I have to admit that I'm confused as to how WA2 determines whether a TGA should represent a selenocysteine or a stop codon in the calculated protein sequence. I look forward to reading the documentation on this later on!
'Move to Opposite Strand' function does not recognize stop codons in display or gff3
issue
created
mpoelchau
username_0
So - is this supposed to be fixed on the demo site (http://icebox.lbl.gov/Apollo2/annotator/index)? Because it doesn't look like it is - I just re-created the same broken model (Name=GB42147-RAa, Group1.1:963204..964163 (961 b), Honey1). Let me know if I'm missing something!
comment
created
nathandunn
username_1
We haven’t updated the server yet.  Sorry. 

Nathan


>
comment
created
nathandunn
username_1
@username_0   I'll update this next week when we tag RC2.   In the interim, it should be on the mainline.
comment
created
mpoelchau
username_0
Great, thanks!
comment
created
mpoelchau
username_0
Looks like it works on icebox now - thanks!
comment
closed
monicacecilia
username_3
issue
created
monicacecilia
username_3
Bingo on RC3. woop woop! (i.e. yes, it works as expected). :dancer:
comment