Open denriquez opened 6 years ago
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
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
Yes, its not initialized after it either.
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,
Is this for a new kit? It use to work