macs2 warnings unknown sequencing problem

Question

[GR]

Hi All,

I have chipseq single-end reads of length 130 bp. From macs2 output I got the warning 'Since the d (229) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem!'.

Can it be because macs2 is not estimating the fragment length correctly? My reads are 130 bp and macs2 calculate the fragment length as 229.

[ivivek_ngs]

is your data paired end or single end? You can always estimate the fragment length from your bam files with the SPP tool which also estimates the quality of your data based on ghost peaks and estimates the fragment length as well. Since you are using the macs2 model so macs2 is estimating the fragment length for you.