{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,6]],"date-time":"2026-07-06T11:52:37Z","timestamp":1783338757088,"version":"3.54.6"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2145,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The sequence alignment\/map format (SAM) is a commonly used format to store the alignments between millions of short reads and a reference genome. Often certain positions within the reads are inherently more likely to contain errors due to the protocols used to prepare the samples. Such biases can have adverse effects on both mapping rate and accuracy. To understand the relationship between potential protocol biases and poor mapping we wrote SAMstat, a simple C program plotting nucleotide overrepresentation and other statistics in mapped and unmapped reads in a concise html page. Collecting such statistics also makes it easy to highlight problems in the data processing and enables non-experts to track data quality over time.<\/jats:p>\n               <jats:p>Results: We demonstrate that studying sequence features in mapped data can be used to identify biases particular to one sequencing protocol. Once identified, such biases can be considered in the downstream analysis or even be removed by read trimming or filtering techniques.<\/jats:p>\n               <jats:p>Availability: SAMStat is open source and freely available as a C program running on all Unix-compatible platforms. The source code is available from http:\/\/samstat.sourceforge.net.<\/jats:p>\n               <jats:p>Contact: \u00a0timolassmann@gmail.com<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq614","type":"journal-article","created":{"date-parts":[[2010,11,19]],"date-time":"2010-11-19T03:58:31Z","timestamp":1290139111000},"page":"130-131","source":"Crossref","is-referenced-by-count":149,"title":["SAMStat: monitoring biases in next generation sequencing data"],"prefix":"10.1093","volume":"27","author":[{"given":"Timo","family":"Lassmann","sequence":"first","affiliation":[{"name":"Omics Science Center, Riken Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yoshihide","family":"Hayashizaki","sequence":"additional","affiliation":[{"name":"Omics Science Center, Riken Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carsten O.","family":"Daub","sequence":"additional","affiliation":[{"name":"Omics Science Center, Riken Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2010,11,18]]},"reference":[{"key":"2023012511155767700_B1","doi-asserted-by":"crossref","first-page":"626","DOI":"10.1038\/ng1789","article-title":"Genome-wide analysis of mammalian promoter architecture and evolution","volume":"38","author":"Carninci","year":"2006","journal-title":"Nat. Genet."},{"key":"2023012511155767700_B2","doi-asserted-by":"crossref","first-page":"1767","DOI":"10.1093\/nar\/gkp1137","article-title":"The Sanger FASTQ file format for sequences with quality scores, and the Solexa\/Illumina FASTQ variants","volume":"38","author":"Cock","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023012511155767700_B3","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1101\/gr.6831208","article-title":"A code for transcription initiation in mammalian genomes","volume":"18","author":"Frith","year":"2008","journal-title":"Genome Res."},{"key":"2023012511155767700_B4","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and Accurate Short Read Alignment with Burrows-Wheeler Transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012511155767700_B5","doi-asserted-by":"crossref","first-page":"1851","DOI":"10.1101\/gr.078212.108","article-title":"Mapping short DNA sequencing reads and calling variants using mapping quality scores","volume":"18","author":"Li","year":"2008","journal-title":"Genome Res."},{"key":"2023012511155767700_B6","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012511155767700_B7","doi-asserted-by":"crossref","first-page":"528","DOI":"10.1038\/nmeth.1470","article-title":"Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan","volume":"7","author":"Plessy","year":"2010","journal-title":"Nat. Methods"},{"key":"2023012511155767700_B8","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1038\/nbt0509-455","article-title":"How to map billions of short reads onto genomes","volume":"27","author":"Trapnell","year":"2009","journal-title":"Nat. Biotechnol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/1\/130\/48861409\/bioinformatics_27_1_130.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/1\/130\/48861409\/bioinformatics_27_1_130.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T11:26:56Z","timestamp":1674646016000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/1\/130\/201972"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,11,18]]},"references-count":8,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2011,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btq614","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2011,1,1]]},"published":{"date-parts":[[2010,11,18]]}}}