Hi. 
I am new for performing RNA-Seq. I have got the sequencing raw reads (PE) for my samples  from Arabidopsis thaliana plants. I have analysed these reads using FASTQC. Now I have to do the alignment and mapping of these reads with the refrence genome. 
In this regard my first question is, should I do any further cleaning or processing for my reads before alignment. And should I have to merge the pair-end reads?
Second question is which aligner should I use? I have tried with BWA, Bowtie2 and STAR, and I got the maximum alignment with STAR.
Other question is which source I should use for the reference genome. Like TAIR10, Araprot11 or ftp://ftp.ensemblgenomes.org/pub/release-41/plants/fasta/arabidopsis_thaliana/dna/

I will be grateful if you may guide me for my analysis. 

Best
Umesh


You should :

 - Not do further cleaning of the fastq files
 - Not merge paired-end fastq files
 - Use STAR for alignment (BWA and bowtie2 are maint for DNA not RNA)
 - For the genome you can use the ENSEMBL version : https://plants.ensembl.org/Arabidopsis_thaliana/Info/Index 