{"id":696,"date":"2014-03-22T15:19:22","date_gmt":"2014-03-22T13:19:22","guid":{"rendered":"http:\/\/bioinfo2.ugr.es\/ceUGR\/?page_id=696"},"modified":"2014-03-22T15:19:22","modified_gmt":"2014-03-22T13:19:22","slug":"ngsmethpipe","status":"publish","type":"page","link":"https:\/\/alu.ugr.es\/bioinfo\/?page_id=696","title":{"rendered":"NGSmethPipe"},"content":{"rendered":"<p><a title=\"NGSmethPipe\" href=\"http:\/\/bioinfo2.ugr.es\/NGSmethPipe\/index.html\" target=\"_blank\"><span style=\"line-height: 1.5em\">NGSmethPipe website<\/span><\/a><\/p>\n<p>NGSmethPipe is a program for the generation of single base-pair-resolution methylation maps from bisulfite conversion high throughput sequencing experiments. The program has 4 steps: <strong>i.<\/strong>\u00a0indexing (sequence conversion into 3 letter alphabet building the Bowtie index), <strong>ii.<\/strong>\u00a0preprocessing of the reads (adapter removal, quality trimming), <strong>iii.<\/strong>\u00a0Bowtie alignment (single-end or pair-end reads) and<strong>\u00a0vi.<\/strong>\u00a0post-processing including SNV and bisulfite failure detection, sequence error handling and extraction of methylation data for different sequence contexts.<\/p>\n<p><strong style=\"color: #000000;line-height: 1.5em\">Main features of NGSmethPipe<\/strong><\/p>\n<p><strong>1.<\/strong> The program implements three quality filters:<strong> i.<\/strong> putative bisulfite failures can be detected,<strong> ii.<\/strong> the false positive rate can be controlled by means of the Phred Scores,<strong> iii.<\/strong> SNV (single nucleotide variants) can be detected and removed.<\/p>\n<p><strong>2.<\/strong> Usage of a &#8220;seed extension&#8221; method applied to the Bowtie alignments allowing\u00a0to map a higher number of reads without compromising the mapping quality.<\/p>\n<p><strong>3.<\/strong> Extensive output options including all possible cytosine sequence contexts ( CG,\u00a0CHG and CHH; where H is A, T or C) and the possibility to join the information from both strands (useful for the detection of hemi-methylation).<\/p>\n<p><strong>4.<\/strong> Complete statistics of the whole process, including aligned reads, discarded reads, discarded positions, chromosome data coverage, etc.<\/p>\n<p><strong>5.<\/strong> The memory and CPU needs can be adapted to the user&#8217;s computer resources.<\/p>\n<p><strong>6.<\/strong> Fastq input files are accepted in zip, gzip, bzip2 or uncompressed.<\/p>\n<p><span style=\"line-height: 1.5em\">[1] Michael Hackenberg, Guillermo Barturen and Jos\u00e9 L. Oliver. 2012.\u00a0<\/span><span style=\"line-height: 1.5em\">DNA Methylation Profiling from High-Throughput Sequencing Data\u00a0<\/span><span style=\"line-height: 1.5em\">In:\u00a0<\/span><strong style=\"line-height: 1.5em\">DNA Methylation &#8211; From Genomics to Technology\u00a0<\/strong><span style=\"line-height: 1.5em\">Dr. Tatiana Tatarinova (Ed.), ISBN: 978-953-51-0320-2, InTech\u00a0<\/span><span style=\"line-height: 1.5em\">[<\/span><a style=\"line-height: 1.5em\" href=\"http:\/\/www.intechopen.com\/download\/pdf\/32798\" target=\"_blank\">PDF<\/a><span style=\"line-height: 1.5em\">]<\/span><\/p>\n","protected":false},"excerpt":{"rendered":"<p>NGSmethPipe website NGSmethPipe is a program for the generation of single base-pair-resolution methylation maps from bisulfite conversion high throughput sequencing experiments. The program has 4 steps: i.\u00a0indexing (sequence conversion into 3 letter alphabet building the Bowtie index), ii.\u00a0preprocessing of the reads (adapter removal, quality trimming), iii.\u00a0Bowtie alignment (single-end or pair-end reads) and\u00a0vi.\u00a0post-processing including SNV and [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":23,"comment_status":"closed","ping_status":"open","template":"","meta":{"footnotes":""},"class_list":["post-696","page","type-page","status-publish","hentry"],"blocksy_meta":[],"_links":{"self":[{"href":"https:\/\/alu.ugr.es\/bioinfo\/index.php?rest_route=\/wp\/v2\/pages\/696","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/alu.ugr.es\/bioinfo\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/alu.ugr.es\/bioinfo\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/alu.ugr.es\/bioinfo\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/alu.ugr.es\/bioinfo\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=696"}],"version-history":[{"count":0,"href":"https:\/\/alu.ugr.es\/bioinfo\/index.php?rest_route=\/wp\/v2\/pages\/696\/revisions"}],"wp:attachment":[{"href":"https:\/\/alu.ugr.es\/bioinfo\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=696"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}