Hi all,
I am new to NGS analysis. I have illumina RNA-seq paird end reads (1.pe1.fastq,2.pe2.fastq,..4.pe1.fastq,4.pe2.fastq) and assembled transcriptome reference sequence(reference.fa). I have aligned the illumina reads (1.pe1.fastq,1.pe2.fastq..4.pe1.fastq,4.pe2.fastq) to the reference transcriptome (reference.fa) using bowtie. Then created mpileup file using samtools. I have predicted SNPs using variant caller varscan. I have found SNPs predicted for each contigs, also with homozygosity & heterozygosity predicted.
1.How can I get distribution of SNPs in each chromosome? (because varscan reports for each contig)
2.From varscan prediction, I get heterozygosity predicted more (about 95%) than heterozygous (5%). I would like know whether my prediction is biologically relevant?
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