deeptools bamcoverage and bamcompare tss plot

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5.1 years ago

zeeshan.fazal1986 ▴ 10

I generated two tss heatmap one from bamcompare and one from bamcoverage big wig files. I did no normalization in any of these. Bamcompare was used with two bams one for IP and one for Input.

I do not under stand bamcompare plot. Anyone please help me to understand this bamcompare plot? why profile plot shows enerichment in negative?

bamcoverage plot: https://photos.google.com/search/_tra_/photo/AF1QipPtl2JzS1By7oWuBK9qxr1suZadPZNNO4Md765C

bamcompare plot: https://photos.google.com/search/_tra_/photo/AF1QipN2X-OVOiDad6GPFRJ1M0lHJ7_OHyxlZaXIgwO4

ChIP-Seq • 1.5k views

ADD COMMENT • link updated 4.1 years ago by grx0326 ▴ 20 • written 5.1 years ago by zeeshan.fazal1986 ▴ 10

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I have the same problem as you do. In IGV the INPUT seems to be lower than the treatment group, but after bamcompare the plot show negative values. Do you have any clues now?

ADD REPLY • link 4.1 years ago by grx0326 ▴ 20

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