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nags.plot.r outputs flat graphs and no results

Hi,

I am running nags.plot.r on my indexed bam files for ChIP-seq data, however the output graphs are blank or flat and I'm struggling to find the reason why. Here are my commands.

For an individual sample:

ngs.plot.r -G dm6 -R genebody -C /Volumes/T7_Touch/FASTA_ChIP/3_bam/ChIP_polIIcontrol_7.bam -O pol_test

Dor a pair of input and sample:

ngs.plot.r -G dm6 -R genebody -C /Volumes/T7_Touch/FASTA_ChIP/3_bam/ChIP_UPF1_3.bam:/Volumes/T7_Touch/FASTA_ChIP/3_bam/ChIP_input_1.bam -O upf1_test3

Any help is greatly appreciated.

Hannah

chip-seq software-error next-gen
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updated by Ram Ram • written by Hannah Dixon • Hannah Dixon

Maybe you can try Deeptools to profile the heatmap

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written by zhuobaowen • zhuobaowen

1 answer

I don't think it supports dm6. You may have to manually get it from their Google Drive. See: https://github.com/shenlab-sinai/ngsplot/wiki/SupportedGenomes

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written by igor igor

Thanks for your comment, I have tried using dm3 with the same outcome. Flat graphs in each attempt and blank heat maps.. Do you think there may be a problem with my Bam files?

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written by Hannah Dixon • Hannah Dixon

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