Hello all,
I am new to ngs (an unfortunately to bioinfo as well) , I Recently sequenced small RNAs (21-29 nt) using Illunina platform. I aligned the reads on to genome using bowtie, and extracted alignments for regions of interest with samtools, I am normalizing data among the samples by counting rRNA reads.
I want to now to count the reads (total number) originating from certain region of genome and plot the read density (for both + and -strands together). Please suggest me any Rpackage or any other suitable method for counting reads and plotting them.
I am new to ngs (an unfortunately to bioinfo as well) , I Recently sequenced small RNAs (21-29 nt) using Illunina platform. I aligned the reads on to genome using bowtie, and extracted alignments for regions of interest with samtools, I am normalizing data among the samples by counting rRNA reads.
I want to now to count the reads (total number) originating from certain region of genome and plot the read density (for both + and -strands together). Please suggest me any Rpackage or any other suitable method for counting reads and plotting them.
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