Hi
I have 6 RNA-Seq samples(same condition,biological replicates) I have used tophat and cufflinks to analysis the samples. I want to know how I can identify the gene density and the percentage of genes transcribed for each chromosome?
Thank you
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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version 2.3.6
Can I run cuffdiff on biological replicates samples and get the gene_exp.diff file?
Yes you can run cuffdiff on biological replicates
I have only one condition, 6 biological replicates. How to get an 'average' gene expression levels of this replicates from cuffdiff?
For gene expression you need two conditions; control and treatment. do you have equal replicates for both conditions?
Currently, I have just one condition with 6 biological replicates and I want to classify genes based on their FPKM values .Do you have any suggestion how I can get an 'average' of FPKM value?
thank you