request for post DNA-mapping pipelines feature

[sunta3iouxos]

Could you please add a string so that we could direct the results of pipelines as ChIP-seq, ATAC-seq etc to a subfolder into the main folder? for example, this is the output of DNA-mapping

 tree /mnt/c/AP01/bamSpikesTESTblackNEW/ -d
/mnt/c/AP01/bamSpikesTESTblackNEW/
├── Bowtie2 -> /mnt/c/AP01/bamSpikesTEST/Bowtie2
├── FASTQ -> /mnt/c/AP01/bamSpikesTEST/FASTQ
├── FASTQ_fastp -> /mnt/c/AP01/bamSpikesTEST/FASTQ_fastp
├── FastQC -> /mnt/c/AP01/bamSpikesTEST/FastQC
├── FastQC_trimmed -> /mnt/c/AP01/bamSpikesTEST/FastQC_trimmed
├── Sambamba -> /mnt/c/AP01/bamSpikesTEST/Sambamba
├── cluster_logs -> /mnt/c/AP01/bamSpikesTEST/cluster_logs
├── deepTools_qc -> /mnt/c/AP01/bamSpikesTEST/deepTools_qc
├── filtered_bam -> /mnt/c/AP01/bamSpikesTEST/filtered_bam
├── multiQC -> /mnt/c/AP01/bamSpikesTEST/multiQC
├── originalFASTQ -> /mnt/c/AP01/bamSpikesTEST/originalFASTQ

If I initiate a ChIP-seq experiment new folders in the /mnt/c/AP01/bamSpikesTESTblackNEW/ will be created. Like split_deepTools_ChIP, etc

I believe it would be nice if those will be by default redirected to subfolders with a default naming of the chosen pipeline+date, or a one defined by a user. So that if we repeat the analysis it can be possible without (re)moving folders.

Thank you

[katsikora]

Hi, if you'd like to obtain results of ChIP-seq or ATAC-seq run with different parameters in different folders, one thing you can do is to provide the bam files from the DNA-mapping workflow e.g. with --fromBAM /path/to/filtered_bams/ --bamExt .filtered.bam. At the same time, specify a custom ouput folder with -d /todays/output, different from the DNA-mapping ouput folder.

Best wishes,

Katarzyna

[sunta3iouxos]

, specify a custom ouput folder with -d /todays/output

I missed that one. But, will it use the same folder as created by the DNA mapping process?

[katsikora]

It will use only the bam files from the folder created by DNA mapping that you point it to. Fragment size metric calculation by deeptools will be repeated for PE reads.