Hi ChIP-seq experts
I'm a newbie in the field of ChIP-seq data mining and need some help! I've sequenced several samples and mapped them using bowtie and everything looks fine so fare
But they differ somewhat in sequence depth which makes them difficult to compare - until now I've used coverageBed (bedtools) to find the read coverage around TSS and in my peak regions and then normalized the read count in these regions to sequence depth.
But for some of my future analysis it would be really nice if the BAM file was normalized to sequence depth - simply, I want to remove some random reads from one sample so it has the same amount of reads as my second sample... I've found that picard "DownsampleSam" should be able to do this, however I cannot get the programme to work on my (mac) computer.
I hope someone can help!!
BR, Kathrine
I'm a newbie in the field of ChIP-seq data mining and need some help! I've sequenced several samples and mapped them using bowtie and everything looks fine so fare
But they differ somewhat in sequence depth which makes them difficult to compare - until now I've used coverageBed (bedtools) to find the read coverage around TSS and in my peak regions and then normalized the read count in these regions to sequence depth.
But for some of my future analysis it would be really nice if the BAM file was normalized to sequence depth - simply, I want to remove some random reads from one sample so it has the same amount of reads as my second sample... I've found that picard "DownsampleSam" should be able to do this, however I cannot get the programme to work on my (mac) computer.
I hope someone can help!!
BR, Kathrine
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