more than 2 replicates can not be used for chips_pipeline about chipseq_pipeline HOT 3 CLOSED

Please remove -trimmed_fastq TRUE first. That flag is for the ATAC-Seq pipeline, not for ChiP-Seq.

The pipeline can take more than two ChiP replicates but number of controls cannot exceed that of ChiP replicates. You can reduce number of controls by merging control fastqs.

For example, first two controls will be merged and then used for ChiP replicate-1, the rest will be merged and used for ChiP replicate-2. Use parameter syntax -ctl_fastq[REP_ID]:[MERGE_ID].

-ctl_fastq1:1 ctrl_islet2.fastq.gz -ctl_fastq1:2 ctrl_islet3.fastq.gz -ctl_fastq2:1 ctrl_islet4.fastq.gz -ctl_fastq2:2 ctrl_islet5.fastq.gz -ctl_fastq2:3 ctrl_islet6.fastq.gz

from chipseq_pipeline.

Thanks. I will try and keep you posted.

Also, atac_dnase_pipelines will generate a json file has a very detailed information. But for chipseq_pipeline the json file does not have as much information as atac_dnase_pipelines does. I am wondering is that because I did not use "python chipseq.py" but "bds chipseq.bds"? Or if I can set any parameters to get a more informative json file too? Thanks.

from chipseq_pipeline.

Or is there any way to using more than 2 replicates? Thanks.

from chipseq_pipeline.