tag:blogger.com,1999:blog-8959227089815463704.post5821855229233885633..comments2023-10-02T17:00:45.520+08:00Comments on Kevin's GATTACA World: PROGRAM: seqtk for sampling, trimming, fastq2fasta, subsequence, reverse complement and moreUnknownnoreply@blogger.comBlogger4125tag:blogger.com,1999:blog-8959227089815463704.post-50005004707088855212012-08-17T17:49:37.612+08:002012-08-17T17:49:37.612+08:00Ah! sorry!
I pasted Li Heng's reply here, per...Ah! sorry! <br />I pasted Li Heng's reply here, perhaps you have the mistaken impression that I am the author of this software. Perhaps that's a question you can direct to the mailling list there? Kevinhttps://www.blogger.com/profile/00419554940694709908noreply@blogger.comtag:blogger.com,1999:blog-8959227089815463704.post-18447539265954703602012-08-17T17:09:42.429+08:002012-08-17T17:09:42.429+08:00Thanks for your reply. So I understand what the Pp...Thanks for your reply. So I understand what the Pphred score means, but what is then considered low quality by "seqtk trimfq"? What is the default and is it possible to choose your own cut-off?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-8959227089815463704.post-80925604423896767062012-08-16T21:10:24.150+08:002012-08-16T21:10:24.150+08:00check out http://en.wikipedia.org/wiki/Phred_qual...check out http://en.wikipedia.org/wiki/Phred_quality_score#Reliability<br />Phred quality scores are defined as a property which is logarithmically related to the base-calling error probabilities .[2]<br /><br />or<br /><br />For example, if Phred assigns a quality score of 30 to a base, the chances that this base is called incorrectly are 1 in 1000. The most commonly used method is to count the bases with a quality score of 20 and aboveKevinhttps://www.blogger.com/profile/00419554940694709908noreply@blogger.comtag:blogger.com,1999:blog-8959227089815463704.post-63226888134927868192012-08-16T19:55:29.784+08:002012-08-16T19:55:29.784+08:00I would like to know what are considered low-quali...I would like to know what are considered low-quality bases by the Phred algorithm.<br />Regards,<br />DennisAnonymousnoreply@blogger.com