Re: Quality Based Trimming

Question: Re: Quality Based Trimming

8.7 years ago by

Florent Angly • 370 wrote:

Thanks for your reply Daniel. That's right... I did not even think about using the boxplot tool to find how much to trim the ends. My reads all have the same length, but still, is seems more natural to only trim as much as needed and no more. For example, I have some reads that are completely low quality and should entirely trimmed/removed, whereas some might of good quality over almost all their length. It's probaby better to use a short sliding window (of, say, 5 bp) and trim the ends until the window has no more than, say zero low quality base pairs. So, the following sequence would be converted from: xxxoxooooooxxooooooxoxxx to: ooooooxxoooooo Florent

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modified 8.7 years ago by Daniel Blankenberg ♦♦ 1.7k • written 8.7 years ago by Florent Angly • 370

8.7 years ago by

Yanwei Tan • 40

Yanwei Tan • 40 wrote:

Hi all, I have a question regarding the trimming length. I would like to trim my the last part 36 bp from my 76 bp reads, then I can compare the result between 36 bp (first part of 76bp) and 76 bp (the whole part). So here I want to ask if I can download the trimed reads from Galaxy. Many thanks! Wei -- Yanwei Tan Institute of Neurobiology 1.OG, AG Bading Im Neuenheimer Feld 364 University of Heidelberg 69120 Heidelberg Germany Tel:+49-6221-548319 Fax:+49-6221-546700

ADD COMMENT • link written 8.7 years ago by Yanwei Tan • 40

Hi Wei, You can download your results from Galaxy at any time by clicking on the Save (disk) icon associated with your dataset, shown after clicking on the dataset's name to expand the view. Thanks for using Galaxy, Dan

ADD REPLY • link written 8.7 years ago by Daniel Blankenberg ♦♦ 1.7k

8.7 years ago by

Daniel Blankenberg ♦♦ 1.7k

United States

Daniel Blankenberg ♦♦ 1.7k wrote:

Hi Florent, Thanks very much for the comments. A sliding window sounds like an excellent approach: allow users to specify the window size, step size, an aggregation action to perform on the window (min, max, sum, mean, etc ), a comparison method (<,<=, ==, etc) and a threshold quality value; allowing users to specify the ends (both or only one or the other) to trim would also likely be useful. Would it also be desirable to allow specifying a number of quality scores that can be excluded from the aggregation action (the zero low quality base pairs in your example)? A window size of 1 would handle the simple case of only trimming the very ends while allowing the user to configure more complex windowing schemes. Thoughts? Thanks, Dan

ADD COMMENT • link written 8.7 years ago by Daniel Blankenberg ♦♦ 1.7k

That sounds perfect Daniel. Advanced options for advanced users, and safe defaults for everyone else will do it. Florent

ADD REPLY • link written 8.6 years ago by Florent Angly • 370

Hi Florent, I've added a tool which will do this to the repository. It is currently available on the test server and will be on the main server next week. Thanks, Dan

ADD REPLY • link written 8.6 years ago by Daniel Blankenberg ♦♦ 1.7k

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