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ATAC SEQ post processing PASS1AC

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Archana Raja edited this page Oct 17, 2022 · 21 revisions
  • ATAC PASS1AC bathes from stanford and Sinai

Croo output paths

Stanford PASS1AC

  • gs://rna-seq_araja/PASS/atac-seq/stanford/PASS1AC/batch*/Output/*/*
  • gs://motrpac-portal-transfer-stanford/Output/atac-seq/batch_20200318/*/*

Sinai PASS1C

  • gs://rna-seq_araja/PASS/atac-seq/sinai/PASS1C/batch*/Output/*/*

Example output data from pass1b

Location for post-processed outputs should be organized batch-wise to make it easy for qc purposes

croo output

  • gs://rna-seq_araja/PASS/atac-seq/sinai/batch4_20210406/Output/
  • gs://rna-seq_araja/PASS/atac-seq/sinai/batch4_20210406/Output/final/

merged outputs from sinai and stanford for pass1b

  • gs://rna-seq_araja/PASS/atac-seq/stanford_sinai_pass1b_merged_results_final

Post-processed outputs should go to paths like these inside each batch folder

  • gs://rna-seq_araja/PASS/atac-seq/sinai/PASS1C/batch*/Output/final

  • gs://rna-seq_araja/PASS/atac-seq/stanford/PASS1AC/batch*/Output/final

  • gs://motrpac-portal-transfer-stanford/Output/atac-seq/batch_20200318/final

  • Atac-seq post-processing wrapper to use (make sure to change the user defined variables) : https://github.com/MoTrPAC/motrpac-atac-seq-pipeline/blob/master/src/atac-post-process_wrapper.sh

  • test the post-processing on one batch first (sinai batch5)

    all the ready to use post-process scripts for each batch can be found in this path (all you have to do is make sure batch_wfids variable points to the file in the right path gs://rna-seq_araja/atac-seq/pp

all the workflow ids batchwise can be found in the below path gs://rna-seq_araja/atac-seq/wfids

  • Pipeline run status

  • due to lack of resources the jobs crashed

  • sinai b5 (rerun merging qaqc report and samtools)

  • sinai b6 (samtools , qaqc merging)

  • sinai b7 (samtools , qaqc merging step)

  • stanford b11 (samtools , qaqc merging step)

  • stanford b12 (samtools, qa-qc merging)

  • stanford b13 (samtools and qa-qc merging)

  • stanford b2 (everything except for generating rep_to_sample_map)

  • Archana to run merged qc on batch6

  • Mihir to finish up samtools for failed samples

  • Archana to test script on PASS1AC merging on couple batches and deploy on all batches

  • Check in the code, merge qa-qc reports from all the batches for release

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