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Forum: Illumina/Solexa 09-09-2016, 08:10 AM
Replies: 8
Views: 1,940
Posted By rEDI
Thank you again for your very helpful answers

Thank you again for your very helpful answers
Forum: Illumina/Solexa 09-09-2016, 08:05 AM
Replies: 8
Views: 1,940
Posted By rEDI
Thank you Fanli. In this case is it however that...

Thank you Fanli. In this case is it however that only 211 bases are covered by both?
Forum: Illumina/Solexa 09-09-2016, 07:58 AM
Replies: 8
Views: 1,940
Posted By rEDI
That is perfect, thank you so much for explaining...

That is perfect, thank you so much for explaining Fanli. That is most helpful

One more question - do the seqs unique to R1 and R2 not merge in this case, or are they merged regardless?

Thank...
Forum: Illumina/Solexa 09-09-2016, 07:41 AM
Replies: 8
Views: 1,940
Posted By rEDI
Hi Fanli Thank you for your answer The...

Hi Fanli

Thank you for your answer

The primer seqs are as follows:

forward
GTGCCAGCCGCCGCGGTAA

reverse
Forum: Illumina/Solexa 09-09-2016, 03:24 AM
Replies: 8
Views: 1,940
Posted By rEDI
Merging illumina V4 paired end reads

Hi

I am having difficulty understanding how my merged reads are producing a certain amplicon size.

Basically, I have 2 x 251bp reads. This 251bp includes primer sequence, of as far as I...
Forum: Illumina/Solexa 05-09-2016, 09:15 AM
Replies: 15
Views: 2,628
Posted By rEDI
Great thanks Thermophile I guess I will...

Great thanks Thermophile

I guess I will include these aspects in my write up, and maybe look to sequence more samples next time.
Forum: Illumina/Solexa 05-09-2016, 08:56 AM
Replies: 15
Views: 2,628
Posted By rEDI
Thanks thermophile - really appreciate it If...

Thanks thermophile - really appreciate it

If that is the case, would sequencing PCR duplicates impact upon the downstream analysis, or preserve pretty much the same trends as rarefying to lower...
Forum: Illumina/Solexa 05-09-2016, 02:21 AM
Replies: 15
Views: 2,628
Posted By rEDI
If anyone could offer some insight into the above...

If anyone could offer some insight into the above comparison between seq depths that would be great

Thank you so much :)
Forum: Illumina/Solexa 05-05-2016, 06:53 AM
Replies: 15
Views: 2,628
Posted By rEDI
Thanks Genomax and Fanli I recently read a...

Thanks Genomax and Fanli

I recently read a paper that sequenced 96 samples of fish gut on MiSeq, with V4 primer set, the exact same as mine.

That study obtained ~3m reads in total after QC....
Forum: Illumina/Solexa 05-05-2016, 06:35 AM
Replies: 15
Views: 2,628
Posted By rEDI
Ok thanks Fanli, will do that for the next sample...

Ok thanks Fanli, will do that for the next sample set

Even still, is rarefying to this higher depth with my current number of samples ok?
Forum: Illumina/Solexa 05-05-2016, 06:29 AM
Replies: 15
Views: 2,628
Posted By rEDI
No, the reads usually plateau after 60k or so per...

No, the reads usually plateau after 60k or so per sample.

I am analyzing fish gut samples.

After v4 sequencing on MiSeq, I get 22m reads for 24 samples. My feeling is that if I sequenced more...
Forum: Illumina/Solexa 05-05-2016, 12:46 AM
Replies: 15
Views: 2,628
Posted By rEDI
Hi Fanli Do you think that rarefying my data...

Hi Fanli

Do you think that rarefying my data to 300k seqs/sample is also ok, or too deep?

In one run I obtained slightly more reads passing filter, and so I rarefied to that sample containing...
Forum: Illumina/Solexa 04-22-2016, 01:23 AM
Replies: 15
Views: 2,628
Posted By rEDI
Thank you Fanli for your answer In another...

Thank you Fanli for your answer

In another study, I rarefied to 300k seqs/sample. Is this also acceptable?

Thank you
Forum: Illumina/Solexa 04-21-2016, 12:40 AM
Replies: 15
Views: 2,628
Posted By rEDI
Sequencing depth

I am sequencing samples from animal gut using illumina MiSeq/HiSeq, targeting the v4 region of the 16S

I get 22m raw reads back from MiSeq (after removal of PhiX etc), for a total of 24 samples.
...
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