Should discodant alignments be retained in ChIP-Seq experiments?

In some online tutorials for ChIP-Seq (1,2) after aligning, non-unique reads are filtered out. However, discordant alignments are not.

Is it standard practice, and why, if so?

chip-seq

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written 5.9 years ago by Aspire 43

Do discordant alignments exist in those tutorials? Usually, ChIP-seq experiments are single-read (not paired-end) so that is not an option.

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written 5.9 years ago by igor 1.3K

These tutorials are indeed single-read. Silly me.

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written 5.9 years ago by Aspire 43

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