Hi everybody, I am trying to align my paired end reads in R using QuasR. everything was easy and smooth until the alignment step. I am using the following line for alignment:
> proj <- qAlign(sampleFile, genome= genomeFile, splicedAlignment= TRUE, alignmentsDir= "bam", clObj = clObj, paired = 'fr')
however there is an error message in the log file says: Error in checkForRemoteErrors(val) : one node produced an error: Error on Galaxy2 processing sample /media//KO_day3_1_1.fq : failed while aligning 25mers
this is happening only when I am applying splicedAlignment=T.
any ideas about what is going on?
thanks much Tamer