Jin wook Lee

Can you share your BAM files for debugging? original: /nfs/nobackup/ensembl/reham_ens/genome/mm10/mm10_enh_dhs.bam processed: /homes/reham/ATAC-Seq/atac_dnase_pipelines/out/align/rep1/mm10_enh_dhs.dupmark.bam.tmp.bam Is your input BAM file filtered/deduped? any quality problem with the input BAM file?

That BED file in the mm10 genome data is not for testing purpose. If you just wanted to test our pipeline. I recommend to use a new pipeline https://github.com/ENCODE-DCC/atac-seq-pipeline.

We recommend to use our new pipeline at https://github.com/ENCODE-DCC/atac-seq-pipeline/. This new pipeline supports docker, DNANexus and Google Cloud platform so that you will avoid any dependency problems. Please read through...

@rehamFatima: Sure, `run_spp.R` is used for cross-correlation analysis. Actual shell command lines are here https://github.com/kundajelab/atac_dnase_pipelines/blob/master/modules/postalign_xcor.bds#L113 What kind of error did you get?

@rehamFatima I actually don't understand why you want to test our pipeline with a BED file (or its BAM conversion) which is not designed to be used as a valid...

Please update your pipeline and reinstall dependencies. This is a known issue and has already been fixed. ``` $ git pull $ bash uninstall_dependencies.sh $ bash install_dependencies.sh ``` After re-installation,...

For those who are suffering from this issue, please reinstall dependencies. This error occurrs when one of the dependencies (`run_spp.R`) is not correctly installed. ``` $ bash uninstall_dependencies.sh $ bash...

This has already been fixed in this commit https://github.com/kundajelab/atac_dnase_pipelines/commit/d110085fcb3d0fdfdf486c94afbdf8aec93ad0e6#diff-46df23ddb8dc0e0db77265566b265050. Please git pull the latest pipeline and try again. Also, this repo has been deprecated. Please try our new pipeline https://github.com/ENCODE-DCC/atac-seq-pipeline/.

Please look into `stderr` and `stdout` files in each task directory `cromwel-executions/atac/RANDOM_HASH_STRING/call-TASK_NAME/shard-?/executions/stderr`. It looks like you ran these pipelines with a local mode (without using docker/singularity). Did you activate Conda...

Yes, chipseq pipeline does not have any adapter-trimming step. Jin