Bam input generated seperatly-cannot run the bds

[Bahareh Haddad Derafshi]

Hi!

I have single end sequencing files from ChIP-seq that I have aligned them my self with bowtie2. 

I am trying to use the sorted and duplicated removed bam files as input to run the bds .

I am trying to use atac.bds and chip.bds , but none of them working.

please let me know if possible to use single ended fast.q files that are converted to bam to use as input for bds run.

Thank you 

Bahareh

[Anshul Kundaje]

The BDS pipelines have been deprecated and replaced with Cromwell pipelines. Please use 

https://github.com/ENCODE-DCC/atac-seq-pipeline

https://github.com/ENCODE-DCC/chip-seq-pipeline2

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[Bahareh Haddad Derafshi]

On Wednesday, December 18, 2019 at 8:01:01 AM UTC-8, Anshul Kundaje wrote:

The BDS pipelines have been deprecated and replaced with Cromwell pipelines. Please use 

https://github.com/ENCODE-DCC/atac-seq-pipeline

https://github.com/ENCODE-DCC/chip-seq-pipeline2

On Tue, Dec 17, 2019, 9:29 PM Bahareh Haddad Derafshi <bahareh...@gmail.com> wrote:

Hi!

I have single end sequencing files from ChIP-seq that I have aligned them my self with bowtie2. 

I am trying to use the sorted and duplicated removed bam files as input to run the bds .

I am trying to use atac.bds and chip.bds , but none of them working.

please let me know if possible to use single ended fast.q files that are converted to bam to use as input for bds run.

Thank you 

Bahareh

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