{"action":"created","issue":{"url":"https://api.github.com/repos/jts/nanopolish/issues/380","repository_url":"https://api.github.com/repos/jts/nanopolish","labels_url":"https://api.github.com/repos/jts/nanopolish/issues/380/labels{/name}","comments_url":"https://api.github.com/repos/jts/nanopolish/issues/380/comments","events_url":"https://api.github.com/repos/jts/nanopolish/issues/380/events","html_url":"https://github.com/jts/nanopolish/issues/380","id":322014715,"number":380,"title":"Polishing no improvement: scrappie related? ","user":{"login":"damientully","id":17030873,"avatar_url":"https://avatars2.githubusercontent.com/u/17030873?v=4","gravatar_id":"","url":"https://api.github.com/users/damientully","html_url":"https://github.com/damientully","followers_url":"https://api.github.com/users/damientully/followers","following_url":"https://api.github.com/users/damientully/following{/other_user}","gists_url":"https://api.github.com/users/damientully/gists{/gist_id}","starred_url":"https://api.github.com/users/damientully/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/damientully/subscriptions","organizations_url":"https://api.github.com/users/damientully/orgs","repos_url":"https://api.github.com/users/damientully/repos","events_url":"https://api.github.com/users/damientully/events{/privacy}","received_events_url":"https://api.github.com/users/damientully/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2018-05-10T17:29:33Z","updated_at":"2018-05-10T17:57:36Z","closed_at":null,"author_association":"NONE","body":"Hi Jared,\r\n\r\nI am trying to polish an assembly that was generated from reads base called using Scrappie. I manually made the .readdb file for indexing the reads and I am highly suscipious of the results given that the polished assembly is no better than the original input. Everything ran fine but I know when I get basecall the reads with Albacore and polish my assembly I do get better accuracy as expected. So although Nanopolish did not complain I think a problem must exist somewhere. Any advice or assistance would be greatly appreciated. \r\n\r\nHere is what I did:\r\n\r\n`$ bwa index Run12_scrappie.contigs.fasta `\r\n\r\n`$ bwa mem -x ont2d -t 10 Run12_scrappie.contigs.fasta Run12_scrappie_reads.fasta | samtools view -Sb - | samtools sort -f - Run12_scrappie.sorted.bam`\r\n`$ samtools index Run12_scrappie.sorted.bam `\r\n\r\n`$ nanopolish variants --consensus Run12_scrappie_polished.fa -w \"tig00000001:1-9036\" -r Run12_scrappie_reads.fasta -b Run12_scrappie.sorted.bam  -g Run12_scrappie.contigs.fasta --fix-homopolymers --min-candidate-frequency 0.1 --ploidy 1\r\n`\r\n\r\n`##fileformat=VCFv4.2\r\n##INFO=<ID=TotalReads,Number=1,Type=Integer,Description=\"The number of event-space reads used to call the variant\">\r\n##INFO=<ID=SupportFraction,Number=1,Type=Float,Description=\"The fraction of event-space reads that support the variant\">\r\n##INFO=<ID=BaseCalledReadsWithVariant,Number=1,Type=Integer,Description=\"The number of base-space reads that support the variant\">\r\n##INFO=<ID=BaseCalledFraction,Number=1,Type=Float,Description=\"The fraction of base-space reads that support the variant\">\r\n##INFO=<ID=AlleleCount,Number=1,Type=Integer,Description=\"The inferred number of copies of the allele\">\r\n##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tsample\r\n[post-run summary] total reads: 28442, unparseable: 0, qc fail: 0, could not calibrate: 0, no alignment: 0, bad fast5: 1\r\n`"},"comment":{"url":"https://api.github.com/repos/jts/nanopolish/issues/comments/388133407","html_url":"https://github.com/jts/nanopolish/issues/380#issuecomment-388133407","issue_url":"https://api.github.com/repos/jts/nanopolish/issues/380","id":388133407,"user":{"login":"damientully","id":17030873,"avatar_url":"https://avatars2.githubusercontent.com/u/17030873?v=4","gravatar_id":"","url":"https://api.github.com/users/damientully","html_url":"https://github.com/damientully","followers_url":"https://api.github.com/users/damientully/followers","following_url":"https://api.github.com/users/damientully/following{/other_user}","gists_url":"https://api.github.com/users/damientully/gists{/gist_id}","starred_url":"https://api.github.com/users/damientully/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/damientully/subscriptions","organizations_url":"https://api.github.com/users/damientully/orgs","repos_url":"https://api.github.com/users/damientully/repos","events_url":"https://api.github.com/users/damientully/events{/privacy}","received_events_url":"https://api.github.com/users/damientully/received_events","type":"User","site_admin":false},"created_at":"2018-05-10T17:57:36Z","updated_at":"2018-05-10T17:57:36Z","author_association":"NONE","body":"It ran in about 10mins. \r\n\r\nAh I may be missing the .gzi and .index file. How do I generate these manually?\r\n\r\nThanks Jared! "}}
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