Enhance doc #47
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archanaraja
commented
Dec 10, 2024
archanaraja
commented
- Added documentation and code to generate tissue specific consensus peak*counts matrix
… matrix - The code and documentation allows user to perform custom consensus peak * counts matrix for their tissue of interest
biodavidjm
reviewed
Dec 13, 2024
README.md
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| @@ -71,7 +71,7 @@ of environment. | |||
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| 5. [Flag problematic samples](#5-flag-problematic-samples) | |||
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| 6. [Post-processing scripts](#6-post-processing-scripts) | |||
| 6. [Pipeline post-processing](#6-post-processing-scripts) | |||
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This has been fixed
biodavidjm
reviewed
Dec 13, 2024
README.md
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| * [encode\_to\_count\_matrix.sh](src/encode_to_count_matrix.sh): use `narrowkpeak.gz` and `tagAlign` files to generate a | ||
| peak x sample raw counts matrix for PASS samples | ||
| * [encode\_to\_count\_matrix_human.sh](src/encode_to_count_matrix_human.sh): use `narrowkpeak.gz` and `tagAlign` files | ||
| to generate a peak x sample raw counts matrix for human samples | ||
| * [align\_stats.sh](src/align_stats.sh): calculate % of primary alignments aligning to chrX, chrY, chrM, autosomes, and | ||
| contigs | ||
| * [merge\_atac\_qc.R](src/merge_atac_qc.R): merge wet lab QC, curated pipeline QC, and alignment stats | ||
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| ### 6.2 Custom analysis |
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I think 6.1 is about processing all tissues simultaneously and 6.2 is for each tissue individually. Something like:
6.1. Generate consensus merged peak and count matrix for all tissues combined
6.2. Generate tissue-specific consensus merged peak and count matrix.
And please, adjust the text to explain it in that way
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All of these suggestions have been incorporated. @biodavidjm
biodavidjm
reviewed
Dec 13, 2024
- Fixed a minor bolding syntax - Added better explanation and descriptions to generate the consensus peak * tissue matrix across all tissues and individual tissues - Fixed the dead link
- Modified description for the atac-post-process-wrapper.sh and atac-seq-human-wrapper.sh
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