Sequence quality drops in the 3' end of the left sequence in paired end. What could be the cause?

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7 months ago

eggrandio ▴ 40

Hello,

We have received the results of a library sequencing and we have noticed that the sequence quality drops at the 3' end of one of the pairs: enter image description here

Moreover, there seems to be a biased base distribution too:

enter image description here

What could be the case? We still have not performed manual filtering of sequences, but I wanted to know what could be causing this.

Anyways, the sequence quality seems somewhat good.

Best,

sequencing • 601 views

ADD COMMENT • link updated 7 months ago by GenoMax 141k • written 7 months ago by eggrandio ▴ 40

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Why Does The Base Quality Drop Towards The End For Illumina Reads ?

ADD REPLY • link 7 months ago by ATpoint 82k

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But shouldn't quality drop at both 3'ends and not just on the left one?

ADD REPLY • link 7 months ago by eggrandio ▴ 40

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This may be one of those things that just happens to be a one-time thing with whatever was going on with this run. Was this sample pooled with others you did not prepare/own?