SYNC ERROR - not all positions converted
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#33 SYNC ERROR - not all positions converted
I've used Popoolation and Popoolation2 in the bast with great success. Now I am trying to use it on a new organism (flu) and from RNA-seq data as opposed to DNA-seq. In examining sync files generated from both the perl and java scripts, I am getting very strange behavior. The perl script outputs 0:0:0:0:0 at ALL positions, while the java script appears to work at some positions but ouputs NULL at others. I am attaching 50 lines of an mpileup file and sync files generated with the following commands:
perl ~/programs/popoolation2_1201/mpileup2sync.pl --input sample.mpileup --output sample_perl.sync
java -ea -Xmx7g -jar ~/programs/popoolation2_1201/mpileup2sync.jar --input sample.mpileup --output sample_java.sync
Any help is appreciated!
Hi,
It may be caused by your encoding setting choice. See the #13 ticket for more informations