splice sites aren't recognized when genomic fasta is lowercase

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splice sites aren't recognized when genomic fasta is lowercase

Monica Poelchau
Hi everyone,

Not sure if this has been reported before. Sometimes, the genomic fasta will contain lower-case sequence (usually when it's soft-masked). Apollo2 will not properly recognize canonical splice sites if the genomic sequence is lower-case. In the following 2 examples, the model is on the + strand:






Monica




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Re: splice sites aren't recognized when genomic fasta is lowercase

nathandunn

We have not seen this before.  I opened a ticket for it here:


Nathan



On Apr 20, 2018, at 2:19 PM, Monica Poelchau <[hidden email]> wrote:

Hi everyone,

Not sure if this has been reported before. Sometimes, the genomic fasta will contain lower-case sequence (usually when it's soft-masked). Apollo2 will not properly recognize canonical splice sites if the genomic sequence is lower-case. In the following 2 examples, the model is on the + strand:

<img src="x-msg://25/?ui=2&amp;ik=cf525517cc&amp;view=att&amp;th=162e4e0741d1d1b7&amp;attid=0.1&amp;disp=safe&amp;realattid=ii_jg8g22zi0_162e4e0741d1d1b7&amp;zw" width="373" height="301" class="">

<img src="x-msg://25/?ui=2&amp;ik=cf525517cc&amp;view=att&amp;th=162e4e0ae3def32b&amp;attid=0.2&amp;disp=safe&amp;realattid=ii_jg8g2e961_162e4e0ae3def32b&amp;zw" width="259" height="295" class="">


Monica



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Re: splice sites aren't recognized when genomic fasta is lowercase

Monica Poelchau
Thanks!

On Fri, Apr 20, 2018 at 3:45 PM, Nathan Dunn <[hidden email]> wrote:

We have not seen this before.  I opened a ticket for it here:


Nathan



On Apr 20, 2018, at 2:19 PM, Monica Poelchau <[hidden email]> wrote:

Hi everyone,

Not sure if this has been reported before. Sometimes, the genomic fasta will contain lower-case sequence (usually when it's soft-masked). Apollo2 will not properly recognize canonical splice sites if the genomic sequence is lower-case. In the following 2 examples, the model is on the + strand:






Monica



This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.







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Re: splice sites aren't recognized when genomic fasta is lowercase

nathandunn

And its fixed and in master.  https://github.com/GMOD/Apollo/pull/1881

Thanks Deepak,

Nathan


On Apr 20, 2018, at 2:46 PM, Monica Poelchau <[hidden email]> wrote:

Thanks!

On Fri, Apr 20, 2018 at 3:45 PM, Nathan Dunn <[hidden email]> wrote:

We have not seen this before.  I opened a ticket for it here:


Nathan



On Apr 20, 2018, at 2:19 PM, Monica Poelchau <[hidden email]> wrote:

Hi everyone,

Not sure if this has been reported before. Sometimes, the genomic fasta will contain lower-case sequence (usually when it's soft-masked). Apollo2 will not properly recognize canonical splice sites if the genomic sequence is lower-case. In the following 2 examples, the model is on the + strand:






Monica



This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.








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