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kundajelab / phantompeakqualtools

This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays.
BSD 3-Clause "New" or "Revised" License
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multiple datasets #5

Open olechnwin opened 7 years ago

olechnwin commented 7 years ago

Hi,

How do you run phantompeakqualtools for multiple dataset? How to specify multiple input files?

leepc12 commented 7 years ago

I think there is no way to do so. run_spp.R does not take multiple input files (tagAlign or bam).

You can run run_spp.R for each dataset (exp. tagAlign/bam and corresponding control tagAlign/bam). Or merge all tagAligns/bams.

Thanks,

Jin

On Mon, Jul 10, 2017 at 1:16 PM, olechnwin notifications@github.com wrote:

Hi,

How do you run phantompeakqualtools for multiple dataset? How to specify multiple input files?

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