I have 20 RICE RNA seq tranascriptome data hiseq 2000 platform paired end reads. I aligned fasta reads with BWA and remove PCR duplicates with PICARD. Later I call SNP with samtools using various parameters. I would like to clarify what parameters should I used while alinging to reference rice genome for looking SNP location 100 bp upstream and 250 bp downstream. I look forward for any positive response.
Rocky
First of all it is not advisable to align the RNAseq read data using BWA. But if your goal if just to pick some handful of polymorphic markers then BWA is fine. Until and unless you feel that you are confident enough to tune the Samtools parameters for the rice genome, I wont tweak the parameters. Once you have the output of samtools in vcf file, you can use tools like annovar or snpEff to annotate the variants w.r.t to the genes position and functional consequences.
ashutoshmits
Thanking you for your speedy response. I have filtered raw data with prinseq and later aligned filtered fasta reads with BWA. Could you please suggest me which tool i.e. ANNOVAR , SNPeff should I use for annotating the SNP called.
Rocky
You can use either of them but I would prefer using snpEff for some reasons I can't explain. You will have to download the annotation database from their website or you have to make one of your own in case they don't have the one for your reference genome.
Hello I have a query regarding SNP vcf file called from SAMtools. ID and FILTER has no values in vcf file. How can we get SNP id for rice? When we do in human genome we refer dbSNP rsID using GATK VarAnnotaor, but in case of rice what should we refer.
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Dear Concern,
I have a query regarding snpEffect variant annotation analysis for castor bean (Ricinus communis) which is unavailable at snpEffect database. How could I make snpEffectPredictor.bin file for castor bean from its genome assembly fasta file available at JCVI http://castorbean.jcvi.org/downloads.php ? I would be glad and highly appreciate for your support.
Rocky
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