{"action":"created","issue":{"url":"https://api.github.com/repos/BenLangmead/bowtie/issues/35","repository_url":"https://api.github.com/repos/BenLangmead/bowtie","labels_url":"https://api.github.com/repos/BenLangmead/bowtie/issues/35/labels{/name}","comments_url":"https://api.github.com/repos/BenLangmead/bowtie/issues/35/comments","events_url":"https://api.github.com/repos/BenLangmead/bowtie/issues/35/events","html_url":"https://github.com/BenLangmead/bowtie/issues/35","id":186767610,"number":35,"title":"Incorrect results when using large index","user":{"login":"mluypaert","id":2804117,"avatar_url":"https://avatars.githubusercontent.com/u/2804117?v=3","gravatar_id":"","url":"https://api.github.com/users/mluypaert","html_url":"https://github.com/mluypaert","followers_url":"https://api.github.com/users/mluypaert/followers","following_url":"https://api.github.com/users/mluypaert/following{/other_user}","gists_url":"https://api.github.com/users/mluypaert/gists{/gist_id}","starred_url":"https://api.github.com/users/mluypaert/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mluypaert/subscriptions","organizations_url":"https://api.github.com/users/mluypaert/orgs","repos_url":"https://api.github.com/users/mluypaert/repos","events_url":"https://api.github.com/users/mluypaert/events{/privacy}","received_events_url":"https://api.github.com/users/mluypaert/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2016-11-02T10:48:02Z","updated_at":"2017-02-01T09:38:15Z","closed_at":null,"body":"I found that when mapping a pair of reads using bowtie 1 (tested with 1.1.1 and 1.1.2), the results when using a large index (a truly large index, not a large-index created from a small fasta) are incorrect.\r\n\r\nThe command used here was: \r\n>bowtie-1.1.1/bowtie --tryhard -a --quiet -X 2000 -v 3 --12 /var/tmp/job_o45b8iO6CN_bowtieIn.tmp Ensembl/Homo_sapiens/release-84/cdna_unspliced/lib > bowtie_o45b8iO6CN_complete_largeidx_output.txt\r\n\r\nTo prove that the large index was the problem, I split the input fasta I used to generate the large index in two parts, and generated small indexes from each part. Then I ran the same bowtie analysis on each small-index part and concatenated the results.\r\n\r\nThe two-part small index analysis returned correct results (see bowtie_o45b8iO6CN_split_merged_output.txt), returning perfect matches on ENST00000551148, ENST00000549155, ENST00000546991, ENST00000392979 and ENST00000392977.\r\nThe large-index analysis however, returned \r\n\r\n* a perfect match for ENST00000551148 and ENST00000549155\r\n* a match with mismatches for ENST00000392977\r\n* no match for ENST00000546991 and ENST00000392979\r\n\r\n[This page](http://genome-euro.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr12%3A100859167%2D100859253&hgsid=218639904_GnqAahapqgTv6gMZNJ30erltl10I) proves that the read-pair from the input file should match perfectly to the five above mentioned transcripts.\r\n\r\nCan anyone please look into this?\r\n\r\nps. I would add the fasta-file I used to generate this large index but the file is 5.8Gb so not fit for upload to github. If you want it, let me know, then we'll see how I could share it.\r\n[bowtie_o45b8iO6CN_complete_largeidx_output.txt](https://github.com/BenLangmead/bowtie/files/566280/bowtie_o45b8iO6CN_complete_largeidx_output.txt)\r\n[bowtie_o45b8iO6CN_split_merged_output.txt](https://github.com/BenLangmead/bowtie/files/566279/bowtie_o45b8iO6CN_split_merged_output.txt)\r\n[job_o45b8iO6CN_bowtieIn.txt](https://github.com/BenLangmead/bowtie/files/566292/job_o45b8iO6CN_bowtieIn.txt)\r\n\r\n\r\n\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/BenLangmead/bowtie/issues/comments/276612987","html_url":"https://github.com/BenLangmead/bowtie/issues/35#issuecomment-276612987","issue_url":"https://api.github.com/repos/BenLangmead/bowtie/issues/35","id":276612987,"user":{"login":"mluypaert","id":2804117,"avatar_url":"https://avatars.githubusercontent.com/u/2804117?v=3","gravatar_id":"","url":"https://api.github.com/users/mluypaert","html_url":"https://github.com/mluypaert","followers_url":"https://api.github.com/users/mluypaert/followers","following_url":"https://api.github.com/users/mluypaert/following{/other_user}","gists_url":"https://api.github.com/users/mluypaert/gists{/gist_id}","starred_url":"https://api.github.com/users/mluypaert/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mluypaert/subscriptions","organizations_url":"https://api.github.com/users/mluypaert/orgs","repos_url":"https://api.github.com/users/mluypaert/repos","events_url":"https://api.github.com/users/mluypaert/events{/privacy}","received_events_url":"https://api.github.com/users/mluypaert/received_events","type":"User","site_admin":false},"created_at":"2017-02-01T09:38:15Z","updated_at":"2017-02-01T09:38:15Z","body":"Hello @ch4rr0 \r\n\r\nI see on the bowtie website that version 1.2.0 was released on 12/12/2016. However I don't see anything in the changelog about the large-index bugfixing (this issue). I assume this was not fixed in release 1.2.0 yet? Any idea on what release would contain this fix and when to expect it to go public?"}}
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