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Question: FastQ sanger sequences -ends quality trimming
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gravatar for rosariobrancaccio
9 months ago by
rosariobrancaccio • 0
rosariobrancaccio • 0 wrote:

Dear all , I'm very naive regarding bioinformatic tools. I need to trim my sanger sequences to remove bad quality 5' and 3' ends and then I will join thiese sequences in order to create a long contig ( each PCR is a piece of a viral genome and I need to recostrunct the whole genome starting from these pcr that I have done with a walk by walk strategy). I tried some tools in galaxy but I'm not able to do the quality treaming of my sequences ( in fastqc i ever see the bad quality ends after the use of trimmomatic or trim galore or others tools. could you suggest me -the right way to do that in galaxy -than I would like to use cap3 to crate the contig ( it's ok?)

suggestions thankss a lot! Petrus
sanger sequences trim galaxy quality • 544 views
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modified 9 months ago by Jennifer Hillman Jackson ♦ 25k • written 9 months ago by rosariobrancaccio • 0
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gravatar for Jennifer Hillman Jackson
9 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

How to trim is covered in this tutorial: https://galaxyproject.org/tutorials/ngs/#trimming-reads

If the final FastQC results reveal that low-quality data is present that you want to be removed, the settings for the trimming tool you are using can be modified, or possibly pick another trimming tool. Each of these QA tools are slightly different. Help is on the tool form or you can find the manuals online (and often tool-specific forums). The same settings used line-command can be set on the Galaxy wrapper's tool form.

Some of this is test > review > test > repeat until the best settings for a set of data are identified. For the test part, I mean to try both permissive and strict settings. It sounds like you are not being aggressive or specific enough for the end clipping.

All Galaxy tutorials, including the above and those for assembly: https://galaxyproject.org/learn/

Thanks! Jen, Galaxy team
ADD COMMENT • link written 9 months ago by Jennifer Hillman Jackson ♦ 25k
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