How can identify the percentage of genes transcribed for each chromosome
1 answer
Tophat-cufflink pipeline produces gene_exp.diff file. Use that file for finding the % of genes transcribed from particular chromosome. The locus field in this file gives information about chromosome and position. You have to filter the genes chromosome-wise and need to get count for each chromosome and calculate percentage.
For gene density, i think you need to pre-define specific window size (say 1 Mbp) and calculate number of genes transcribed in that region.
MySQL will be better approach for this analysis.
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