rnaAlign.sh: rnaStrand variable never gets initialized

[PedalheadPHX]

Is this for a new kit? It use to work

[ryanrichholt]

Yea, thats really confusing because I don't see it initialized in the oldest version of the script either: https://github.com/tgen/pegasusPipe/blob/54c06cffb419bc5a64a7df6c98a51a17572d0094/pegasus_rnaAlign.sh

[ryanrichholt]

It's this chunk you're talking about right? rnaStrand is not initialized anywhere before this section.

if [[ $rnaStrand == "FIRST" || $rnaStrand == "SECOND" ]] ; then
    echo "##running stranded STAR case"
    qsub -A $debit -l nodes=1:ppn=$nCores -v RGTAGLIST="'"$rgTagList"'",SAMNAME=$samName,SAMTOOLSPATH=$samtoolsPath,STARPATH=$starPath,STARREF=$starRef,STARGTF=$starGTF,FASTQL1="'"$fastqList1"'",FASTQL2="'"$fastqList2"'",DIR=$ownDir,NXT1=$nxtStep1,NXT2=$nxtStep2,NXT3=$nxtStep3,NXT4=$nxtStep4,NXT5=$nxtStep5,NXT6=$nxtStep6,NXT7=$nxtStep7,NXT8=$nxtStep8,NXT9=$nxtStep9,NXT10=$nxtStep10,NXT11=$nxtStep11,RUNDIR=$runDir,RNASTRAND=$rnaStrand,D=$d $pbsHome/pegasus_strandedStar.pbs
    if [ $? -eq 0 ] ; then
        touch $ownDir.starInQueue
    else
        ((qsubFails++))
    fi
    sleep 2
else
    echo "##running unstranded STAR case"
    echo "qsub -A $debit -l nodes=1:ppn=$nCores -v RGTAGLIST="'"$rgTagList"'",SAMNAME=$samName,SAMTOOLSPATH=$samtoolsPath,STARPATH=$starPath,STARREF=$starRef,STARGTF=$starGTF,FASTQL1="'"$fastqList1"'",FASTQL2="'"$fastqList2"'",DIR=$ownDir,NXT1=$nxtStep1,NXT2=$nxtStep2,NXT3=$nxtStep3,NXT4=$nxtStep4,NXT5=$nxtStep5,NXT6=$nxtStep6,NXT7=$nxtStep7,NXT8=$nxtStep8,NXT9=$nxtStep9,NXT10=$nxtStep10,RUNDIR=$runDir,RNASTRAND=$rnaStrand,D=$d $pbsHome/pegasus_star.pbs"
    qsub -A $debit -l nodes=1:ppn=$nCores -v RGTAGLIST="'$rgTagList'",SAMNAME=$samName,SAMTOOLSPATH=$samtoolsPath,STARPATH=$starPath,STARREF=$starRef,STARGTF=$starGTF,FASTQL1="'$fastqList1'",FASTQL2="'$fastqList2'",DIR=$ownDir,NXT1=$nxtStep1,NXT2=$nxtStep2,NXT3=$nxtStep3,NXT4=$nxtStep4,NXT5=$nxtStep5,NXT6=$nxtStep6,NXT7=$nxtStep7,NXT8=$nxtStep8,NXT9=$nxtStep9,NXT10=$nxtStep10,NXT11=$nxtStep11,RUNDIR=$runDir,RNASTRAND=$rnaStrand,D=$d $pbsHome/pegasus_star.pbs
    if [ $? -eq 0 ] ; then
        touch $ownDir.starInQueue
    else
        ((qsubFails++))
    fi
sleep 2
fi

[denriquez]

Yes, its not initialized after it either.

[PedalheadPHX]

Does STAR care about strand of the library, My recollection is there is no difference in running STAR with stranded or not, unlike tophat which does care. but it is needed for the expression estimates with cufflinks, ht-seq, salmon, sailfish,