I recently run into a problem in my ChIP-seq data as it has low alignment rate to the mm9 genome. It turned out that a large number of the reads contain adapter sequences. We haven't applying adapter trimming to our analysis since we can get a decent alignment most of the time. But in this case, I do need to trim the adapters. I have tired cutadapt and it seems to work well.
My question is on how to control the length of the reads after adapter trimming. Does it make a big difference if I don't control anything (i.e. keep everything that is left after trimming adapters?
Thanks.
My question is on how to control the length of the reads after adapter trimming. Does it make a big difference if I don't control anything (i.e. keep everything that is left after trimming adapters?
Thanks.
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