Welcome to the MapMan Family of Software Forum

Please do not hesitate to register and post your question.

Don't forget to subscribe to your posted message so you get notified on updates.
Every question you post will help others and or enhance the software!

Post a question,   post a bug!

Welcome to the MapMen Family of Software Forum Welcome to the MapMen Family of Software Forum

Using MapMan

sugarcane

sugarcane
mercator fasta upload problem mercator
Answer
1/8/17 10:09 PM
Hi

I'm trying to use mapman for NCBI sugarcane protein fasta file.I tried using the mercator pipeline assign MapMan "Bins" to arbitrary protein input sequences. However it fails to start because it keeps finding sequences in the fasta file it fails to interpret. I’ve tried correcting these problems, but while the interface shows the file has 17 fatal errors it only shows one error at a time, which means you need to keep resubmitting the file. Is it possible to get mercaptor to ignore entries it can't interpret or get it to report all the erroneous entries so I can remove them from the file.


Thanks

RE: sugarcane
Answer
1/9/17 7:47 AM as a reply to Edmond J Breen.
Hi


as a workaround you can plain mail them to me, so I can check them.
usadel .. bio1.rwth-aachen.de

Björn

RE: sugarcane
Answer
1/10/17 1:01 AM as a reply to Björn Usadel.
Thanks for the offer, but tried MercFastaValidation which produced a useable fasta file.


Björn Usadel:
Hi


as a workaround you can plain mail them to me, so I can check them.
usadel .. bio1.rwth-aachen.de

Björn

RE: sugarcane
Answer
1/9/17 8:21 AM as a reply to Edmond J Breen.
Hi Edmond,

I have a prototype validator which will create a 'mercator valid' fasta file..

you can access it here - you need to upload your fasta file, and the tool will generate a list of error (but more importantly, generate a downloadable fasta file).

Please bear in mind that this is still in the testing phase.

http://dev.plabipd.de/portal/mercfastavalidation

Regards,
Marie.

RE: sugarcane
Answer
1/10/17 12:59 AM as a reply to Marie Bolger.
Thanks for this it worked great.


Marie Bolger:
Hi Edmond,

I have a prototype validator which will create a 'mercator valid' fasta file..

you can access it here - you need to upload your fasta file, and the tool will generate a list of error (but more importantly, generate a downloadable fasta file).

Please bear in mind that this is still in the testing phase.

http://dev.plabipd.de/portal/mercfastavalidation

Regards,
Marie.