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

Hi Tamer
What is your read length? SpliceMap (the aligner used, when 'splicedAlignment= TRUE') struggles with reads shorter than 50nts, see also: SpliceMap in QuasR package failing when sorting 25mer-alignments

As a workaround, I recommend to use STAR to create the BAM files outside of QuasR and then create the qproject with a sample file listing the BAM files (see QuasR vignete: 5.1 Create a sample file)

Regards, Hans-Rudolf