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Old 02-10-2014, 03:40 PM   #1
hweeing
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Default What is your threshold for QC?

Hello everybody,

I am really new to this field and trying to learn to use Galaxy.

Just wondering if there is any criteria used to determine the "right" quality of data and at what threshold do you discard or trim your sequences? In what situation will you decide to trim?

I used the FastQC in galaxy
will you trim the first 10 bases for the per base content below? GC content, Kmer content has fluctuation for the first 10 bases.
http://130.102.155.19/datasets/5cb89...ce_content.png

any advice?
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Old 02-10-2014, 04:02 PM   #2
dexterslab
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Is this RNA-Seq data?
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Old 02-10-2014, 04:09 PM   #3
hweeing
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that's right
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Old 02-10-2014, 04:23 PM   #4
GenoMax
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It is normal to see this kind of a pattern with RNA-seq data. See post #18 for some links: http://seqanswers.com/forums/showthread.php?t=13582 One more thread with useful info: http://seqanswers.com/forums/showthread.php?t=13902

Normally you should not need to do any trimming (because of this nucleotide distribution) and can go on to the alignment step.

Last edited by GenoMax; 02-10-2014 at 04:26 PM.
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Old 02-10-2014, 04:27 PM   #5
JackieBadger
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If you are SNP calling bring in QC criteria for the locus and surrounding bases.
I wouldn't go below Q20 (http://en.wikipedia.org/wiki/Phred_quality_score). Using Q criteria become more important at low coverage (depth) nucleotides.
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Old 02-10-2014, 04:29 PM   #6
hweeing
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So, even if the program flagged error for these few parameters doesnt really matter much, unless the Phred score <20. Cool. thanks!
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