Dear all,
I carried out a ChIP-seq experiment for which I have fastq files for both the input and the ChIPped DNA. As expected, I reckon, the input sample produced many more reads than the ChIP sample. The former also have a better quality than the latter. After trimming (to remove the low-quality 3' ends of the reads) I'm left with 35 n-long sequences. If I align these reads to my reference genome using bowtie (bowtie -n 3 -l 35 --tryhard --best) the % of reads with at least one reported alignment is 96% for my Input DNA but only 45% for my ChIPped DNA. Is this normal? Or am I missing something?
Thanks for your help.
Nico
I carried out a ChIP-seq experiment for which I have fastq files for both the input and the ChIPped DNA. As expected, I reckon, the input sample produced many more reads than the ChIP sample. The former also have a better quality than the latter. After trimming (to remove the low-quality 3' ends of the reads) I'm left with 35 n-long sequences. If I align these reads to my reference genome using bowtie (bowtie -n 3 -l 35 --tryhard --best) the % of reads with at least one reported alignment is 96% for my Input DNA but only 45% for my ChIPped DNA. Is this normal? Or am I missing something?
Thanks for your help.
Nico
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