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,


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