Re: [galaxy-user] Extracting number of reads from Bowtie analysis

Hello, Simple counts can be obtained from the tool "NGS: SAM Tools -> flagstat". Other options are "NGS: Picard (beta) -> BAM Index Statistics" for statistics about hits per chromosome in target genome. And the Picard tool "BAM Index Statistics" offers still another set of statistics. The Pic

[galaxy-user] Extracting number of reads from Bowtie analysis

Hello, I am new here! I am aligning Solexa files to genome using tool: NGS: Mapping: Map with Bowtie for Illumina. My question: What is the most easy way to check the number of aligned reads in the output from above? I couldn't find this number directly. I found a way, but it looks circula