Question: Transcriptome analysis for differential gene expression
1
gravatar for umeshtanwar2
6 weeks ago by
umeshtanwar210
umeshtanwar210 wrote:

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

rna-seq • 118 views
ADD COMMENTlink modified 6 weeks ago by Nicolas Rosewick7.3k • written 6 weeks ago by umeshtanwar210
3
gravatar for Nicolas Rosewick
6 weeks ago by
Belgium, Brussels
Nicolas Rosewick7.3k wrote:

You should :

ADD COMMENTlink written 6 weeks ago by Nicolas Rosewick7.3k

Thank you Nicolas Rosewick for your kind help.

ADD REPLYlink written 6 weeks ago by umeshtanwar210
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