Hi users,
I am trying to get an idea of the coverage of my Illumina GA2 experiment on a 3Mb fragment, and I thought of counting reads aligned at each position of my reference sequence and then plotting to get a visual graph. Does this actually make any sense? Is there any tool that does this already or do I have to get my poor scripting abilities in use here? For example maqview shows alignment but it is difficult to see coverage and actually it is difficult to see the coverage for the whole fragment. And I usually see "reduced" figures i narticles showing general coverage.
I have read of people setting windows of a certain width for calculating coverage but I think counting at each position might be more informative
Any hints or pointers would be great!
Cheers,
Dave
I am trying to get an idea of the coverage of my Illumina GA2 experiment on a 3Mb fragment, and I thought of counting reads aligned at each position of my reference sequence and then plotting to get a visual graph. Does this actually make any sense? Is there any tool that does this already or do I have to get my poor scripting abilities in use here? For example maqview shows alignment but it is difficult to see coverage and actually it is difficult to see the coverage for the whole fragment. And I usually see "reduced" figures i narticles showing general coverage.
I have read of people setting windows of a certain width for calculating coverage but I think counting at each position might be more informative
Any hints or pointers would be great!
Cheers,
Dave
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