QuasR error message
Last seen 2.0 years ago
Frankfurt am Main
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
• 405 views
Last seen 4 months ago
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)
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