chip seq data visualization

Question

[nswati106]

So im using bigwig files (generated from bedgrpah files which are output for macs2) of certain histone enrichment marks to check whether that mark is enriched in different categories of genes, im plotting plot profile and boxplot of this data but when im using bamcompare to make bigwig file(log2ratio chip/input), the results are not matching. Now Im not sure which will be correct representation of enrichmemt data, plots plotted from bigwig file generated from macs2 or log2ratioIP/Input from bamcompare? And also values are more toward negative in bw file generated from bamcompare in comaprison to bigwig file(bdg IP/bdg input using bdgcompare).

[LChart]

It would be helpful to see:

(1) some IGV tracks of:

. (a) raw histone (deduplicated coverage) tracks

. (b) raw input/IgG (deduplicated coverage) tracks

. (c) macs2 signal tracks

. (d) bamcompare normalized tracks

(2) fragment length distributions (if paired-end)

(3) dotplot of macs2-normalized vs bacompare-normalized (bin or peak coverage using e.g. deeptools)

[nswati106]

Thanks, i'll put screenshots soon of the plots you suggested. Do have a look if possible. but what do you mean by raw histone(deduplicated coverage ) tracks. Rest i understood

[LChart]

Remove duplicate reads/pairs from your bam and run bedtools genomecov or equivalent.

[nswati106]

OK.I'll try and put the screenshot