{"record_type":"pith_number_record","schema_url":"https://pith.science/schemas/pith-number/v1.json","pith_number":"pith:2011:Z6JQL3JZJZQSEJJJ2GFSXUOXMK","short_pith_number":"pith:Z6JQL3JZ","schema_version":"1.0","canonical_sha256":"cf9305ed394e61222529d18b2bd1d762b8821014fcedf1312db3e175fcddf6ef","source":{"kind":"arxiv","id":"1109.5681","version":3},"attestation_state":"computed","paper":{"title":"Quantifying uniformity of mapped reads","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":[],"primary_cat":"q-bio.GN","authors_text":"Adam Roberts, Lior Pachter, Richard Starfield, Valerie Hower","submitted_at":"2011-09-26T19:33:37Z","abstract_excerpt":"Summary: We describe a tool for quantifying the uniformity of mapped reads in high-throughput sequencing experiments. Our statistic directly measures the uniformity of both read position and fragment length, and we explain how to compute a p-value that can be used to quantify biases arising from experimental protocols and mapping procedures. Our method is useful for comparing different protocols in experiments such as RNA-Seq.\n  Availability and Implementation: We provide a freely available and open source python script that can be used to analyze raw read data or reads mapped to transcripts i"},"verification_status":{"content_addressed":true,"pith_receipt":true,"author_attested":false,"weak_author_claims":0,"strong_author_claims":0,"externally_anchored":false,"storage_verified":false,"citation_signatures":0,"replication_records":0,"graph_snapshot":true,"references_resolved":false,"formal_links_present":false},"canonical_record":{"source":{"id":"1109.5681","kind":"arxiv","version":3},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.GN","submitted_at":"2011-09-26T19:33:37Z","cross_cats_sorted":[],"title_canon_sha256":"5316358474e22e40bdde577e821c70611959b7ddae2a5271d4b5b029cf75dcda","abstract_canon_sha256":"c2c7f6f1c6dcb07d6206479347480a20cf4063435efc34df380d695d95bd8719"},"schema_version":"1.0"},"receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-05-18T03:10:00.613673Z","signature_b64":"ldNUR1pJREHmNixpkT19U4Wwj/w9nsdApGcC/XlUF7VV9BIEk96bm0qFhA+Y36pyKO5PyOBM8bRdcJmBaKnoBg==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"cf9305ed394e61222529d18b2bd1d762b8821014fcedf1312db3e175fcddf6ef","last_reissued_at":"2026-05-18T03:10:00.613224Z","signature_status":"signed_v1","first_computed_at":"2026-05-18T03:10:00.613224Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"graph_snapshot":{"paper":{"title":"Quantifying uniformity of mapped reads","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":[],"primary_cat":"q-bio.GN","authors_text":"Adam Roberts, Lior Pachter, Richard Starfield, Valerie Hower","submitted_at":"2011-09-26T19:33:37Z","abstract_excerpt":"Summary: We describe a tool for quantifying the uniformity of mapped reads in high-throughput sequencing experiments. Our statistic directly measures the uniformity of both read position and fragment length, and we explain how to compute a p-value that can be used to quantify biases arising from experimental protocols and mapping procedures. Our method is useful for comparing different protocols in experiments such as RNA-Seq.\n  Availability and Implementation: We provide a freely available and open source python script that can be used to analyze raw read data or reads mapped to transcripts i"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1109.5681","kind":"arxiv","version":3},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"references":{"count":0,"sample":[],"resolved_work":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","internal_anchors":0},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"},"aliases":[{"alias_kind":"arxiv","alias_value":"1109.5681","created_at":"2026-05-18T03:10:00.613283+00:00"},{"alias_kind":"arxiv_version","alias_value":"1109.5681v3","created_at":"2026-05-18T03:10:00.613283+00:00"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1109.5681","created_at":"2026-05-18T03:10:00.613283+00:00"},{"alias_kind":"pith_short_12","alias_value":"Z6JQL3JZJZQS","created_at":"2026-05-18T12:26:47.523578+00:00"},{"alias_kind":"pith_short_16","alias_value":"Z6JQL3JZJZQSEJJJ","created_at":"2026-05-18T12:26:47.523578+00:00"},{"alias_kind":"pith_short_8","alias_value":"Z6JQL3JZ","created_at":"2026-05-18T12:26:47.523578+00:00"}],"events":[],"event_summary":{},"paper_claims":[],"inbound_citations":{"count":0,"internal_anchor_count":0,"sample":[]},"formal_canon":{"evidence_count":0,"sample":[],"anchors":[]},"links":{"html":"https://pith.science/pith/Z6JQL3JZJZQSEJJJ2GFSXUOXMK","json":"https://pith.science/pith/Z6JQL3JZJZQSEJJJ2GFSXUOXMK.json","graph_json":"https://pith.science/api/pith-number/Z6JQL3JZJZQSEJJJ2GFSXUOXMK/graph.json","events_json":"https://pith.science/api/pith-number/Z6JQL3JZJZQSEJJJ2GFSXUOXMK/events.json","paper":"https://pith.science/paper/Z6JQL3JZ"},"agent_actions":{"view_html":"https://pith.science/pith/Z6JQL3JZJZQSEJJJ2GFSXUOXMK","download_json":"https://pith.science/pith/Z6JQL3JZJZQSEJJJ2GFSXUOXMK.json","view_paper":"https://pith.science/paper/Z6JQL3JZ","resolve_alias":"https://pith.science/api/pith-number/resolve?arxiv=1109.5681&json=true","fetch_graph":"https://pith.science/api/pith-number/Z6JQL3JZJZQSEJJJ2GFSXUOXMK/graph.json","fetch_events":"https://pith.science/api/pith-number/Z6JQL3JZJZQSEJJJ2GFSXUOXMK/events.json","actions":{"anchor_timestamp":"https://pith.science/pith/Z6JQL3JZJZQSEJJJ2GFSXUOXMK/action/timestamp_anchor","attest_storage":"https://pith.science/pith/Z6JQL3JZJZQSEJJJ2GFSXUOXMK/action/storage_attestation","attest_author":"https://pith.science/pith/Z6JQL3JZJZQSEJJJ2GFSXUOXMK/action/author_attestation","sign_citation":"https://pith.science/pith/Z6JQL3JZJZQSEJJJ2GFSXUOXMK/action/citation_signature","submit_replication":"https://pith.science/pith/Z6JQL3JZJZQSEJJJ2GFSXUOXMK/action/replication_record"}},"created_at":"2026-05-18T03:10:00.613283+00:00","updated_at":"2026-05-18T03:10:00.613283+00:00"}