problem with QuasR alignment

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

rna-seq chip-seq quasr

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updated 8.7 years ago by Biostar

• written 8.8 years ago by ta_awwad

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