tag:blogger.com,1999:blog-6282293920238017122.post2378642486642414323..comments2024-03-02T00:18:22.263-08:00Comments on The Sense Strand: An in-depth look at data quality (Part 1)Rosie Redfieldhttp://www.blogger.com/profile/06807912674127645263noreply@blogger.comBlogger3125tag:blogger.com,1999:blog-6282293920238017122.post-72433785524976986152015-01-11T19:24:51.725-08:002015-01-11T19:24:51.725-08:001)The way I worded the "aligned to only 20% o...1)The way I worded the "aligned to only 20% of the genome" was indeed awkward, and I've updated the post to correct it.<br /><br />2)I'm not discarding that sample (yet), I just didn't include it in that graph because it caused scaling problems to the graph as a whole.<br /><br />3)You're right, we don't know what the GC% of the transcriptome is. Intuitively, 40% is what I would expect but I realize now I really have no evidence to support that.Scott M.https://www.blogger.com/profile/11261987412133675499noreply@blogger.comtag:blogger.com,1999:blog-6282293920238017122.post-58734476036585368352015-01-11T16:24:31.464-08:002015-01-11T16:24:31.464-08:00I don't think we know the 'expected value&...I don't think we know the 'expected value' for %G+C of the pooled mRNAs.Rosie Redfieldhttps://www.blogger.com/profile/06807912674127645263noreply@blogger.comtag:blogger.com,1999:blog-6282293920238017122.post-61098513087975439652015-01-11T16:22:04.348-08:002015-01-11T16:22:04.348-08:00You wrote "Note that one sample was aligned ...You wrote "Note that one sample was aligned to only 20% of the genome and is not on the graph." This doesn't make any biological sense and it doesn't fit its context either, so I think you probably mean that 20% of the reads aligned to the genome. <br /><br />If this is the correct interpretation then we shouldn't discard the data without more measures of whether or not it will be informative.Rosie Redfieldhttps://www.blogger.com/profile/06807912674127645263noreply@blogger.com