I often heard that "alignment of sequence reads to a reference can be inaccurate towards the ends of a read", does anybody know the exact reason of this?
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written
by
freeheart.steven •
One reason would be that the quality of the reads gets dropped at the end. Its because of the sequencing chemistry.
Hence for e.g, a 100 bp read will have low quality bases at the end (10-20 bases). Its good to see the box plot of quality score and trim off the bases if necessary before alignment.
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written
by
GouthamAtla
Why quality of the reads gets dropped at the end?
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written
by
lakhujanivijay
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Cross-posted on SeqAnswers