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Old 06-24-2014, 07:15 PM   #21
Brian Bushnell
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BBDuk can trim a set number of bases on the left or right side of a read. However, there are some library-prep protocols that are biased, especially near the read start, and thus have suspicious base-frequency histograms, even though they are correct. So, before you trim, I suggest you map the reads to a reference (even the lowest-quality assembly is OK) to determine whether there is actually a higher error rate in the first X bases of the read. If not, then you should not trim them.

With an assembly, you can determine it like this:

bbmap.sh in=reads.fq mhist=mhist.txt qhist=qhist.txt

This will give you histograms of the average qualities by read position, and match/substitution/insertion/deletion/N rates by read position. That will allow you to determine whether the stated read quality is accurate, and thus whether you need to trim the ends of reads.

If you want to trim a set number of bases on each side, you can use BBDuk's "ftl" (force-trim left) and "ftr" (force-trim right) flags to set the limits of where to trim.
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Old 06-25-2014, 09:51 PM   #22
Brian Bushnell
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The fragmentation sites may be biased, depending on how fragmentation was done. Try mapping with BBMap and using the 'mhist' output, which shows the error rate by read position. If the error rate on the 5' end is not much higher than anywhere else, there's no need to trim it.
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Old 09-20-2016, 07:03 PM   #23
arkanion
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Use Trimmomatic
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Old 01-11-2018, 12:34 AM   #24
liguanghao
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I use TrimGalore to trim adapter and the fastqc result also show that there are biases in 5' end, several kmers occurring.
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