Peak statistics in QC reports

[encode-dcc]

Peak statistics in QC reports

[leepc12]

You can simply ignore raw peak stats.
We will hide it from the report in the next release v1.1.6 (commit e68b6b8).
It's redundant.

[nicolerg]

Can you also include both IDR and naive peak set stats in the JSON?

[akundaje]

Yes good idea. We should do that in the JSON

…

On Thu, Jan 10, 2019, 2:20 PM nicolerg ***@***.*** wrote: Can you also include both IDR and naive peak set stats in the JSON? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#74 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAI7EepiTCrXcuu5QtKRJrgi2E21NlkNks5vB5JygaJpZM4Z6Hrc> .

[nicolerg]

Hi @leepc12, was this issue fixed across all implementations of the pipeline? I no longer get erroneous raw peak ataqc stats when I run the pipeline locally with conda, but a collaborator who ran the v1.1.7 pipeline on GCP has the same bug in her JSON report.

[leepc12]

Yes, this is already fixed in v1.1.6.

Example qc.json from v1.1.6 run:
https://github.com/ENCODE-DCC/atac-seq-pipeline/blob/master/test/test_workflow/ref_output/v1.1.6/ENCSR356KRQ_subsampled/qc.json#L427

Can you upload her qc.json file?

[nicolerg]

Just this line:

            "Raw peaks": [
                74269, 
                "OK"
            ], 

{
    "general": {
        "date": "2019-03-20 10:11:14", 
        "pipeline_ver": "v1.1.7", 
        "peak_caller": "macs2", 
        "genome": "rn6.tsv", 
        "description": "ATAC-seq on MoTrPAC", 
        "title": "20180725_5_Liver_002_powder_S4", 
        "paired_end": [
            true
        ]
    }, 
    "flagstat_qc": {
        "rep1": {
            "total": 92694432, 
            "total_qc_failed": 0, 
            "duplicates": 0, 
            "duplicates_qc_failed": 0, 
            "mapped": 92123522, 
            "mapped_qc_failed": 0, 
            "mapped_pct": 99.38, 
            "paired": 51743818, 
            "paired_qc_failed": 0, 
            "read1": 25871909, 
            "read1_qc_failed": 0, 
            "read2": 25871909, 
            "read2_qc_failed": 0, 
            "paired_properly": 50741198, 
            "paired_properly_qc_failed": 0, 
            "paired_properly_pct": 98.06, 
            "with_itself": 51103330, 
            "with_itself_qc_failed": 0, 
            "singletons": 69578, 
            "singletons_qc_failed": 0, 
            "singletons_pct": 0.13, 
            "diff_chroms": 78236, 
            "diff_chroms_qc_failed": 0
        }
    }, 
    "dup_qc": {
        "rep1": {
            "unpaired_reads": 0, 
            "paired_reads": 20329998, 
            "unmapped_reads": 0, 
            "unpaired_dupes": 0, 
            "paired_dupes": 6863253, 
            "paired_opt_dupes": 6353, 
            "dupes_pct": 0.337592
        }
    }, 
    "pbc_qc": {
        "rep1": {
            "total_read_pairs": 20329998, 
            "distinct_read_pairs": 13483546, 
            "one_read_pair": 10166059, 
            "two_read_pair": 2492700, 
            "NRF": 0.663234, 
            "PBC1": 0.75396, 
            "PBC2": 4.078332
        }
    }, 
    "nodup_flagstat_qc": {
        "rep1": {
            "total": 26933490, 
            "total_qc_failed": 0, 
            "duplicates": 0, 
            "duplicates_qc_failed": 0, 
            "mapped": 26933490, 
            "mapped_qc_failed": 0, 
            "mapped_pct": 100.0, 
            "paired": 26933490, 
            "paired_qc_failed": 0, 
            "read1": 13466745, 
            "read1_qc_failed": 0, 
            "read2": 13466745, 
            "read2_qc_failed": 0, 
            "paired_properly": 26933490, 
            "paired_properly_qc_failed": 0, 
            "paired_properly_pct": 100.0, 
            "with_itself": 26933490, 
            "with_itself_qc_failed": 0, 
            "singletons": 0, 
            "singletons_qc_failed": 0, 
            "singletons_pct": 0.0, 
            "diff_chroms": 0, 
            "diff_chroms_qc_failed": 0
        }
    }, 
    "overlap_reproducibility_qc": {
        "Nt": 0, 
        "N1": 127461, 
        "Np": 0, 
        "N_opt": 127461, 
        "N_consv": 127461, 
        "opt_set": "rep1-pr", 
        "consv_set": "rep1-pr", 
        "rescue_ratio": 0.0, 
        "self_consistency_ratio": 1.0, 
        "reproducibility": "pass"
    }, 
    "idr_reproducibility_qc": {
        "Nt": 0, 
        "N1": 74269, 
        "Np": 0, 
        "N_opt": 74269, 
        "N_consv": 74269, 
        "opt_set": "rep1-pr", 
        "consv_set": "rep1-pr", 
        "rescue_ratio": 0.0, 
        "self_consistency_ratio": 1.0, 
        "reproducibility": "pass"
    }, 
    "frip_macs2_qc": {
        "rep1": {
            "FRiP": 0.312998501123
        }, 
        "rep1-pr1": {
            "FRiP": 0.317969240676
        }, 
        "rep1-pr2": {
            "FRiP": 0.322046516961
        }
    }, 
    "overlap_frip_qc": {
        "rep1-pr": {
            "FRiP": 0.241691255014
        }
    }, 
    "idr_frip_qc": {
        "rep1-pr": {
            "FRiP": 0.190524844719
        }
    }, 
    "ataqc": {
        "rep1": {
            "Genome": "Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa.gz", 
            "Paired/Single-ended": "Paired-ended", 
            "Read length": 75, 
            "Read count from sequencer": 92694432, 
            "Read count successfully aligned": 92123522, 
            "Read count after filtering for mapping quality": 59637527, 
            "Read count after removing duplicate reads": 52774274, 
            "Read count after removing mitochondrial reads (final read count)": 26933490, 
            "NRF": [
                0.663234, 
                "out of range [0.8, inf]"
            ], 
            "PBC1": [
                0.75396, 
                "out of range [0.8, inf]"
            ], 
            "PBC2": [
                4.078332, 
                "OK"
            ], 
            "picard_est_library_size": 31429662, 
            "Fraction of reads in NFR": [
                0.499886971921, 
                "OK"
            ], 
            "NFR / mono-nuc reads": [
                1.53787093978, 
                "out of range [2.5, inf]"
            ], 
            "Presence of NFR peak": "OK", 
            "Presence of Mono-Nuc peak": "OK", 
            "Presence of Di-Nuc peak": "OK", 
            "Raw peaks": [
                74269, 
                "OK"
            ], 
            "Naive overlap peaks": [
                127461, 
                "OK"
            ], 
            "IDR peaks": [
                74269, 
                "OK"
            ], 
            "Naive peak stats: Min size": 150.0, 
            "Naive peak stats: 25 percentile": 325.0, 
            "Naive peak stats: 50 percentile (median)": 495.0, 
            "Naive peak stats: 75 percentile": 760.0, 
            "Naive peak stats: Max size": 4715.0, 
            "Naive peak stats: Mean": 577.525611756, 
            "IDR peak stats: Min size": 150.0, 
            "IDR peak stats: 25 percentile": 441.0, 
            "IDR peak stats: 50 percentile (median)": 651.0, 
            "IDR peak stats: 75 percentile": 913.0, 
            "IDR peak stats: Max size": 4715.0, 
            "IDR peak stats: Mean": 706.594002881, 
            "TSS_enrichment": 6.25728227255
        }
    }
}

[nicolerg]

In the example you linked to, why is the number of raw peaks less than the number of IDR peaks?

[leepc12]

Thanks for reporting this. The term Raw peaks is internally equal to "IDR peaks" in the ataqc module. We will remove it in the next release or hotfix.