ChIP-seq analysis when fragment size is a range of 300 to 700 bp

[ickou]

Hi

I have a question about ChIP-seq analysis.

Usually, in a ChIP-seq experiment, we have a sonication fragment size of 320 bp (200 bpwithout adaptors) and we use this value in MACS for the band width (--bw).
After, MACS uses the "d" parameter to shift tags... (shiftsize = 100 pb)

But, I have a new experiment where sonication fragment size is a range of 300 to 700 bp... a smear was cut out from the gel instead of a narrowband.

Can I analyze this experiment with MACS? other software? what value for the band width? correct d value to shift tags? Do you know any publication about this case?

thank you for your experience returns.

Ickou

[NextGenSeq]

We just did a comparison of RIP-Seq using small sheared cDNA and unsheared cDNA.

Larger fragments show a huge amount of bias. If it were me I would reshear the DNA prior to the ChIP.