{"action":"created","issue":{"url":"https://api.github.com/repos/sdparekh/zUMIs/issues/91","repository_url":"https://api.github.com/repos/sdparekh/zUMIs","labels_url":"https://api.github.com/repos/sdparekh/zUMIs/issues/91/labels{/name}","comments_url":"https://api.github.com/repos/sdparekh/zUMIs/issues/91/comments","events_url":"https://api.github.com/repos/sdparekh/zUMIs/issues/91/events","html_url":"https://github.com/sdparekh/zUMIs/issues/91","id":380754879,"node_id":"MDU6SXNzdWUzODA3NTQ4Nzk=","number":91,"title":"Is the phred cutoff for barcodes also applied to the cDNA read?","user":{"login":"MaxKman","id":30081989,"node_id":"MDQ6VXNlcjMwMDgxOTg5","avatar_url":"https://avatars1.githubusercontent.com/u/30081989?v=4","gravatar_id":"","url":"https://api.github.com/users/MaxKman","html_url":"https://github.com/MaxKman","followers_url":"https://api.github.com/users/MaxKman/followers","following_url":"https://api.github.com/users/MaxKman/following{/other_user}","gists_url":"https://api.github.com/users/MaxKman/gists{/gist_id}","starred_url":"https://api.github.com/users/MaxKman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MaxKman/subscriptions","organizations_url":"https://api.github.com/users/MaxKman/orgs","repos_url":"https://api.github.com/users/MaxKman/repos","events_url":"https://api.github.com/users/MaxKman/events{/privacy}","received_events_url":"https://api.github.com/users/MaxKman/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2018-11-14T15:36:24Z","updated_at":"2018-11-15T11:51:27Z","closed_at":null,"author_association":"NONE","body":"Hey,\r\n\r\nI still enjoy using zUMIs. Our last run was a bit overclustered, not too bad but read2 had a few lower quality bases at the end in a larger fraction of the reads. The sequencing quality of read1 was unaffected and way higher than a phred20 cutoff for nearly all reads. I noticed that with standard settings zUMIs included only 251,475,031 of 462,222,869 reads int the mapping stage. When I reduced BC_filter and UMI_filter to phred10 nearly all reads were used for mapping and I ended up with a much better dataset. In figure 1 of your paper it looks as if both barcodes and cDNA get filtered based on a phred score cutoff. But can I set these seperately, or is the one cutoff set for the barcodes used for the cDNA as well?\r\n\r\nAlso, a sidenote (don't want to open up a new topic for that): the detected cells plot in the stats folder regularly crashes adobe reader because it includes too many individual data points. Might be better to include that in a rasterized format.\r\n\r\nThanks for developing zUMIs and best regards\r\nMax\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/sdparekh/zUMIs/issues/comments/439014636","html_url":"https://github.com/sdparekh/zUMIs/issues/91#issuecomment-439014636","issue_url":"https://api.github.com/repos/sdparekh/zUMIs/issues/91","id":439014636,"node_id":"MDEyOklzc3VlQ29tbWVudDQzOTAxNDYzNg==","user":{"login":"sdparekh","id":29371559,"node_id":"MDQ6VXNlcjI5MzcxNTU5","avatar_url":"https://avatars3.githubusercontent.com/u/29371559?v=4","gravatar_id":"","url":"https://api.github.com/users/sdparekh","html_url":"https://github.com/sdparekh","followers_url":"https://api.github.com/users/sdparekh/followers","following_url":"https://api.github.com/users/sdparekh/following{/other_user}","gists_url":"https://api.github.com/users/sdparekh/gists{/gist_id}","starred_url":"https://api.github.com/users/sdparekh/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sdparekh/subscriptions","organizations_url":"https://api.github.com/users/sdparekh/orgs","repos_url":"https://api.github.com/users/sdparekh/repos","events_url":"https://api.github.com/users/sdparekh/events{/privacy}","received_events_url":"https://api.github.com/users/sdparekh/received_events","type":"User","site_admin":false},"created_at":"2018-11-15T11:51:27Z","updated_at":"2018-11-15T11:51:27Z","author_association":"OWNER","body":"Hi Max,\r\nI made a perl script to simply check the barcode fastq file for the number of reads that would filter for give threshold. It only takes barcode fastq file and checks for the number of bases and phred threshold specified. \r\n\r\nYou run it with the following command and you get the number of raw and filtered reads as stdout.\r\n\r\nperl fqfilter_check.pl barcoderead.filtered.fastq.gz 1 30 1 30 1-12 13-20\r\nRaw reads: 2484156 \r\nFiltered reads: 2287051 \r\n\r\nSince i can not attack a file with .pl extension, i am uploading it as .txt but please save it as a perl script before using.\r\n\r\nLet me know if you find different numbers with this script. This would be the quickest check for your issue.\r\n\r\nBest,\r\nSwati\r\n[fqfilter_check.txt](https://github.com/sdparekh/zUMIs/files/2585142/fqfilter_check.txt)\r\n"}}
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