Unexpected number of reads at the end ..

[ptranvan]

Hi,

I have a MP which contain 27 912 951 reads.
After nexclip, categories A+B+C contain 8 458 324 reads
And categories D+E = 3 569 827 reads

It looks like it misses 27 912 951 - (8 458 324 + 3 569 827) = 15 884 800

Where are those reads ??

[richardmleggett]

Hi Patrick,

Not sure... can you send the complete output text from NextClip to richard.leggett@earlhan.ac.ukmailto:richard.leggett@earlhan.ac.uk and I'll look into it.

Thanks,
Richard

On 10 Aug 2016, at 09:51, Patrick Tran Van <notifications@github.commailto:notifications@github.com> wrote:

Hi,

I have a MP which contain 27 912 951 reads.
After nexclip, categories A+B+C contain 8 458 324 reads
And categories D+E = 3 569 827 reads

It looks like it misses 27 912 951 - (8 458 324 + 3 569 827) = 15 884 800

Where are those reads ??

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[richardmleggett]

Hi,

I've just looked at your log file.

The issue is that you have a LOT of reads that are too short after clipping. You can see this in the line:

All categories too short: 15884800 56.91 %

which is towards the bottom of the log. The minimum length is, by default, 25 bp.

I note that you also have a very high level of PCR duplicates too.

All the best,
Richard

On 10 Aug 2016, at 09:51, Patrick Tran Van <notifications@github.commailto:notifications@github.com> wrote:

Hi,

I have a MP which contain 27 912 951 reads.
After nexclip, categories A+B+C contain 8 458 324 reads
And categories D+E = 3 569 827 reads

It looks like it misses 27 912 951 - (8 458 324 + 3 569 827) = 15 884 800

Where are those reads ??

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Reply to this email directly, view it on GitHubhttps://github.com//issues/20, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AAWKvp3YYfkwUzVxpKBbqL4hf4GjanIoks5qeZEagaJpZM4Jg67E.

[ptranvan]

I see ... Thanks

Another questions, what are the categories D and E, can I use them as paired end reads ?

[richardmleggett]

Hi Patrick,

Category D reads don't contain the adaptor in either read. Category E reads are reads which don't appear to contain the adaptor, but by relaxing the match criteria, we can find what may be the adaptor. Category E reads are usually a small number and I would ignore. I also tend not to use category D reads, as without the presence of a junction adaptor, it is unclear what has happened.

So the safe approach is just to use category A, B and C.

Thanks,
Richard

On 10 Aug 2016, at 11:56, Patrick Tran Van <notifications@github.commailto:notifications@github.com> wrote:

I see ... Thanks

Another questions, what are the categories D and E, can I use them as paired end reads ?

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