Closed chklopp closed 11 years ago
rbuels
commented
11 years ago Definitely sounds like a bug somewhere in the BAM handling. Would you be able to send me a link to your JBrowse instance that exhibits the problem so I could look at it directly?
chklopp
commented
11 years ago http://genotoul.toulouse.inra.fr/~klopp/JBrowse-1.8.1/index.html?data=Test4665765767 Choose scaffold1 position 6500 to 9500.
The reads are not in line with the prediction because of the soft clips.
Le 29/03/2013 15:00, Robert Buels a écrit :
Definitely sounds like a bug somewhere in the BAM handling. Would you be able to send me a link to your JBrowse instance that exhibits the problem so I could look at it directly?
— Reply to this email directly or view it on GitHub https://github.com/GMOD/jbrowse/issues/229#issuecomment-15641897.
= Christophe KLOPP BIA INRA Toulouse = = CS 52627 31326 Castanet-Tolosan = = Tel: 33 5 61 28 50 36 Email: christophe.klopp@toulouse.inra.fr = = http://www.sigenae.org/ =
rbuels
commented
11 years ago I tried just now and could not connect to it. Is the server down?
chklopp
commented
11 years ago Try,
http://genoweb.toulouse.inra.fr/~klopp/JBrowse-1.8.1/index.html?data=Test4665765767
Cheers,
Christophe
Robert Buels notifications@github.com a écrit :
I tried just now and could not connect to it. Is the server down?
Reply to this email directly or view it on GitHub: https://github.com/GMOD/jbrowse/issues/229#issuecomment-15721809
rbuels
commented
11 years ago I'm having a problem viewing the BAM files on that server, I think you might have Apache's mime_magic module enabled, see: http://www.gmod.org/wiki/JBrowse_Configuration_Guide#Apache_Configuration_Note
chklopp
commented
11 years ago Here is the picture I get from IGV for scaffold1:6505..9962
Cheers
Christophe
Le 02/04/2013 15:39, Robert Buels a écrit :
I'm having a problem viewing the BAM files on that server, I think you might have Apache's mime_magic module enabled, see: http://www.gmod.org/wiki/JBrowse_Configuration_Guide#Apache_Configuration_Note
— Reply to this email directly or view it on GitHub https://github.com/GMOD/jbrowse/issues/229#issuecomment-15775357.
= Christophe KLOPP BIA INRA Toulouse = = CS 52627 31326 Castanet-Tolosan = = Tel: 33 5 61 28 50 36 Email: christophe.klopp@toulouse.inra.fr = = http://www.sigenae.org/ =
rbuels
commented
11 years ago Could you try again to attach the IGV picture to the issue? It didn't come through.
rbuels
commented
11 years ago The server issue seems fixed now, though.
rbuels
commented
11 years ago i think this is probably fixed now in master, the fix will be coming out in JBrowse 1.9.0
chklopp
commented
11 years ago Hi,
I still get the same result using the latest code of the master. Th code contains the latest modification linked in git.
Cheers
Christophe
Le 02/04/2013 23:36, Robert Buels a écrit :
i think this is probably fixed now in master, the fix will be coming out in JBrowse 1.9.0
— Reply to this email directly or view it on GitHub https://github.com/GMOD/jbrowse/issues/229#issuecomment-15804256.
= Christophe KLOPP BIA INRA Toulouse = = CS 52627 31326 Castanet-Tolosan = = Tel: 33 5 61 28 50 36 Email: christophe.klopp@toulouse.inra.fr = = http://www.sigenae.org/ =
rbuels
commented
11 years ago Try clearing your browser's javascript cache.
Hi,
I've upload a RNA-Seq bam file in a local instance of jbrowse 1.8.1. The spliced reads are not well positionned on the reference. It seems that the alignments having a soft clip at the begining of the cigar line are not correctly placed.
Is there script to run before adding the bam track?
Christophe