{"id":2515,"date":"2015-05-28T05:51:54","date_gmt":"2015-05-28T05:51:54","guid":{"rendered":"http:\/\/41j.com\/blog\/?p=2515"},"modified":"2015-05-28T06:04:03","modified_gmt":"2015-05-28T06:04:03","slug":"basic-bowtie2-alignment-notes","status":"publish","type":"post","link":"https:\/\/41j.com\/blog\/2015\/05\/basic-bowtie2-alignment-notes\/","title":{"rendered":"Basic bowtie2 alignment notes"},"content":{"rendered":"<p>It&#8217;s equally been a while since I&#8217;ve driven bowtie, and now there&#8217;s bowtie2. Basic alignment notes:<\/p>\n<pre class=\"brush: bash; title: ; notranslate\" title=\"\">\r\n.\/bowtie2-build ~\/genomics\/myreferece.fasta myreference\r\n<\/pre>\n<pre class=\"brush: bash; title: ; notranslate\" title=\"\">\r\n.\/bowtie2 -x myreference -q myreads.fastq -S .\/al.sam\r\n<\/pre>\n<p>And out pops a SAM file. This can be converted to a BAM with samtools:<\/p>\n<pre class=\"brush: plain; title: ; notranslate\" title=\"\">\r\n.\/samtools faidx ~\/genomics\/myreference.fasta\r\n.\/samtools import ~\/genomics\/myreference.fasta.fai .\/al.sam .\/al.bam\r\n<\/pre>\n","protected":false},"excerpt":{"rendered":"<p>It&#8217;s equally been a while since I&#8217;ve driven bowtie, and now there&#8217;s bowtie2. Basic alignment notes: .\/bowtie2-build ~\/genomics\/myreferece.fasta myreference .\/bowtie2 -x myreference -q myreads.fastq -S .\/al.sam And out pops a SAM file. This can be converted to a BAM with samtools: .\/samtools faidx ~\/genomics\/myreference.fasta .\/samtools import ~\/genomics\/myreference.fasta.fai .\/al.sam .\/al.bam<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_publicize_message":"","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2}},"categories":[1],"tags":[],"class_list":["post-2515","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"jetpack_publicize_connections":[],"jetpack_featured_media_url":"","jetpack_shortlink":"https:\/\/wp.me\/p1RRoU-Ez","jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/posts\/2515","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/comments?post=2515"}],"version-history":[{"count":3,"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/posts\/2515\/revisions"}],"predecessor-version":[{"id":2518,"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/posts\/2515\/revisions\/2518"}],"wp:attachment":[{"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/media?parent=2515"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/categories?post=2515"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/41j.com\/blog\/wp-json\/wp\/v2\/tags?post=2515"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}