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Zhang-lab / ATAC-seq_QC_analysis

Atac-seq QC matrix
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Use another genome not in your references #3

Open El-Castor opened 4 years ago

El-Castor commented 4 years ago

Hi,

I want to used your software to do a QC on my ATACseq data performed on cucumis melo species. I'm wondering if it's possible and how I can integrate my genome on your image ?

Thanks in advances

ShaopengLiu1 commented 4 years ago

Hello,

Yes, it's possible (but a little trivial)

  1. Please see here for what resource files you will need: https://github.com/Zhang-lab/ATAC-seq_QC_analysis/blob/master/pipe_code/qc_source.sh, briefly you need: BWA-ref, chrom_size, black_list (make an empty file if you don't have this), promoter file, coding promoter file and genome size parameter for macs2 (https://github.com/taoliu/MACS)

  2. create all the files locally, then bind the folder path into Singularity -B <path-to-parent-folder-of-ref-file>:/atac_seq/Resource/Genome

  3. modify the qc_source.sh file to add your local reference files (you may need to create a new image) to store the updated file.

Or if you can give me your script for generating all of those files above, I can add to the reference genome from my side, which would be more friendly for you to use

El-Castor commented 4 years ago

Hello,

Thanks for your response, I' ve a question : what do you mean for promoter file and coding promoter, I mean what is the difference between the two file. coding_promoter are the promoter of the only coding gene ? and the promoter_file it's all the promoter of the genome features ?

Thanks

Le mar. 15 oct. 2019 à 02:20, Shaopeng Liu notifications@github.com a écrit :

Hello,

Yes, it's possible (but a little trivial)

1.

Please see here for what resource files you will need: https://github.com/Zhang-lab/ATAC-seq_QC_analysis/blob/master/pipe_code/qc_source.sh, briefly you need: BWA-ref, chrom_size, black_list (make an empty file if you don't have this), promoter file, coding promoter file and genome size parameter for macs2 (https://github.com/taoliu/MACS) 2.

create all the files locally, then bind the folder path into Singularity -B

:/atac_seq/Resource/Genome 3. modify the qc_source.sh file to add your local reference files (you may need to create a new image) to store the updated file. Or if you can give me your script for generating all of those files above, I can add to the reference genome from my side, which would be more friendly for you to use — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub , or unsubscribe .
ShaopengLiu1 commented 4 years ago

Yes, coding promoter is the promoter regions of only coding gene, for ATAC-seq (open chromatin) coding genes, they usually have stronger signals.

Promoter file is for all gene features (including but more than coding gene). The relatively lower enrichment signal of non-coding genes will lead to a lower enrichment level.

ShaopengLiu1 commented 4 years ago

The image build files are here if you need: "https://github.com/Zhang-lab/ATAC-seq_QC_analysis/tree/master/image_build_file"

I am trying to add a personlized input file as a parameter, should update soon, this will make your process easier.