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ENCODE-DCC / chip-seq-pipeline2

ENCODE ChIP-seq pipeline
MIT License
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custom aligner option disappeared in v1.5.0 #170

Open Flowdihow opened 4 years ago

Flowdihow commented 4 years ago

Hi Jin,

it seems that the custom aligner/peak options have disappeared in the last two releases. May I ask, why this is the case?

We are investigating to which extend the pipeline can be used for other technologies as well (such as CUT&RUN). In this respect, we would like to try different bowtie parameters. Is there a chance to achieve this?

Thank you very much Best, Florian

akundaje commented 4 years ago

This should be supported.

@Jin - can you reactivate this and update the documentation.

Thanks

On Thu, Jul 2, 2020, 5:32 AM Flowdihow notifications@github.com wrote:

Hi Jin,

it seems that the custom aligner/peak options have disappeared in the last two releases. May I ask, why this is the case?

We are investigating to which extend the pipeline can be used for other technologies as well (such as CUT&RUN). In this respect, we would like to try different bowtie parameters. Is there a chance to achieve this?

Thank you very much Best, Florian

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Flowdihow commented 4 years ago

Hi Yin & Anshul,

Thanks for your support!

Best, Flo

leepc12 commented 3 years ago

Could you please check if this WDL on branch PIP-1287_reenable_custom_aligner works with your custom aligner? Added custom_align_py and custom_aligner_idx_tar back to the code.

Flowdihow commented 3 years ago

Hi Yin,

sorry for coming back to you so late. Everything works fine as expected!

Thanks Flo