Help with plotting ngs (small RNA seq) data

[Ami]

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.

[adamdeluca]

I would:
1. use bedtools to convert bam to a bedgraph file
2. convert the bedgraph to bigwig (ucsc utility)
3. place bigwig on a web server
4. point UCSC genome browser at bigwig file

[Kennels]

You could use:

Galaxy (web based tools, http://main.g2.bx.psu.edu/)

Integrated Genome Viewer (get .sam format from bowtie, convert to .bam using samtools, use coverage tool in IGV and also plot it there),

SeqMonk (another integrated software that can do this),

Artemis (may be somewhat confusing to learn initially, but have some flexible plotting tools (using 'User graphs' option),

R bioconductor for sequence analysis (http://www.bioconductor.org/help/wor...ut-sequencing/)

[NicoBxl]

I use bowtie -> Sam -> Bam -> IGV

[Ami]

Thank you everybody for the help, I am trying the suggested options to find out which is easy for me.