{"action":"created","issue":{"url":"https://api.github.com/repos/transcript/samsa2/issues/3","repository_url":"https://api.github.com/repos/transcript/samsa2","labels_url":"https://api.github.com/repos/transcript/samsa2/issues/3/labels{/name}","comments_url":"https://api.github.com/repos/transcript/samsa2/issues/3/comments","events_url":"https://api.github.com/repos/transcript/samsa2/issues/3/events","html_url":"https://github.com/transcript/samsa2/issues/3","id":317356300,"number":3,"title":"Where is the File 2 (R2) or reverse file in the script?","user":{"login":"camilleberrocal","id":38699681,"avatar_url":"https://avatars1.githubusercontent.com/u/38699681?v=4","gravatar_id":"","url":"https://api.github.com/users/camilleberrocal","html_url":"https://github.com/camilleberrocal","followers_url":"https://api.github.com/users/camilleberrocal/followers","following_url":"https://api.github.com/users/camilleberrocal/following{/other_user}","gists_url":"https://api.github.com/users/camilleberrocal/gists{/gist_id}","starred_url":"https://api.github.com/users/camilleberrocal/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/camilleberrocal/subscriptions","organizations_url":"https://api.github.com/users/camilleberrocal/orgs","repos_url":"https://api.github.com/users/camilleberrocal/repos","events_url":"https://api.github.com/users/camilleberrocal/events{/privacy}","received_events_url":"https://api.github.com/users/camilleberrocal/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2018-04-24T19:05:50Z","updated_at":"2018-04-29T19:25:46Z","closed_at":"2018-04-29T19:25:46Z","author_association":"NONE","body":"I’ve been looking at the master_script.sh of SAMSA2 and I’ve noticed that the line to identify the reverse file or the R2 file is not really clear. Instead it shows an echo for the file 1 (R1) and ‘awk’ command that will out-put a file with a printed name of R2. \r\n\r\nConsidering that two independent files exist, for reverse and forward sequences and SAMSA2 can call out one of the files, why does it not call file 2 (R2)?\r\n\r\n\r\n------------------------------------------------------------------------------------\r\n STEP 1: MERGING OF PAIRED-END FILES USING PEAR\r\n Note: paired-end files are usually named using R1 and R2 in the name.\r\n\t\tExample: control_1.R1.fastq\r\n\t\t\t\t control_1.R2.fastq\r\n\r\n Note: if using single-end sequencing, skip this step (comment out).\r\n Note: if performing R analysis (step 6), be sure to name files with\r\n \tthe appropriate prefix (\"control_$file\" and \"experimental_$file\")!\r\n\r\ncd $starting_files_location\r\nfor file in $starting_files_location/*.gz\r\ndo\r\n\tgunzip $file\r\ndone\r\n\r\nfor file in $starting_files_location/*_R1*\r\ndo\r\n\tfile1=$file\r\n\t**file2=`echo $file1 | awk -F \"R1\" '{print $1 \"R2\" $2}'`\r\n\tout_path=`echo $file | awk -F \"_R1\" '{print $1 \".merged\"}'`\r\n\tout_name=`echo ${out_path##*/}`**\r\n\t\r\n\t$pear_location/pear -f $file1 -r $file2 -o $out_name\r\ndone\r\n\r\nmkdir $starting_location/step_1_output/\r\nmv $starting_files_location/*merged* $starting_location/step_1_output/\r\necho -e \"\\nPaired-end merging step completed.\\n\"\r\n\r\n#################################################################### \r\n\r\n\r\nI would like to know what exactly is the command doing for file 2 (R2) ? \r\n\r\n\r\nThank you for your time, \r\nCamille "},"comment":{"url":"https://api.github.com/repos/transcript/samsa2/issues/comments/385274971","html_url":"https://github.com/transcript/samsa2/issues/3#issuecomment-385274971","issue_url":"https://api.github.com/repos/transcript/samsa2/issues/3","id":385274971,"user":{"login":"camilleberrocal","id":38699681,"avatar_url":"https://avatars1.githubusercontent.com/u/38699681?v=4","gravatar_id":"","url":"https://api.github.com/users/camilleberrocal","html_url":"https://github.com/camilleberrocal","followers_url":"https://api.github.com/users/camilleberrocal/followers","following_url":"https://api.github.com/users/camilleberrocal/following{/other_user}","gists_url":"https://api.github.com/users/camilleberrocal/gists{/gist_id}","starred_url":"https://api.github.com/users/camilleberrocal/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/camilleberrocal/subscriptions","organizations_url":"https://api.github.com/users/camilleberrocal/orgs","repos_url":"https://api.github.com/users/camilleberrocal/repos","events_url":"https://api.github.com/users/camilleberrocal/events{/privacy}","received_events_url":"https://api.github.com/users/camilleberrocal/received_events","type":"User","site_admin":false},"created_at":"2018-04-29T19:25:46Z","updated_at":"2018-04-29T19:25:46Z","author_association":"NONE","body":"Thank you so much I appreciate the clarification! \r\nI go it now.\r\nIt's rearranging the name before calling the variable. \r\n\r\nThanks!\r\n "}}
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