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 Picard tools have more stringent requirements on BAM files. Converting SAM -> BAM with SAMTool, with headers, will produce a sorted BAM file within Galaxy.
There are options that can make the alignment process more sensitive, but these can make the Bowtie job much slower, so much so that these are not recommended for the main Galaxy public server (the job risks timing out, although this does also depend on the quality/size of the query data). Starting with high quality, groomed, data is the best
Hopefully this helps, Jen Galaxy team On 3/12/12 9:08 AM, Jerzy Dyczkowski wrote:
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 circular and unoptimal: to run Bowtie with option: put umapped reads into the file, download the file, open it, count reads, subtract from reads in the original file. However, downloading large files is time-consuming, and I am sure the easier way is somewhere. Further question: good link to help on how to improve number of reads from ChIP study aligned to mouse genome would be also appreciated. best regards, Jerzy ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
