I have been using macs2 for peak calling and posterior differential peak calling. I am working with paired-end data. After calling peaks with macs2 callpeak -B option i use macs2 bdgdiff for differential analysis.
I have observed that, for some contrasts, results look better when I do not use -BAMPE option in the first call to "callpeak". Is that a normal behavior?
When running bdgdiff I have to set the -c (cutoff) at 45 to get reasonable results. Also values in the log ratio of likelihood in the output range from very high values (10³⁵) to very big negative values. Is this the cutoff a reasonable value? are this results normal?
Thank you very much,
Lucas
•
written
by
lucas.michel •
1 answer
If you have paired reads then you need to use -f BAMPE, otherwise only the 5' read of each pair will be used and cross-correlation will be used to estimate fragment length, as opposed to using the actual fragment lengths between pairs. Have you compared the 'd' value for each analysis?
I haven't used bdgdiff, in favour of MANORM, diffReps, or DiffBind. diffReps can do without replicates, but diffReps cannot.
Log in to answer this question.
-
Use of IDR after running MACS3 for ATAC-seq data
written by Orange •
-
macs2 output r file not generated
written by mavy •
-
MACS2 not working in paired end mode
written by Filago •
-
MACS2: broad and broad no-model output peaks are exactly the same. Is something wrong?
written by piyushjo
-
ChipSeq using MACS2 - option to not call peaks with only few reads ?
written by Bastien Hervé
-
MACS2 produces different results using BAMPE and BEDPE
written by Marius •
-
MACS callpeak no summit location with --broad option
written by AlicePsyche •
-
Extension size problem in MACS2
written by anu014
-
MACS2 call differential binding events
written by sophialovechan •
-
Empty output from MACS2 when using control
written by lm687
