Forum: Illumina/Solexa
07-02-2019, 01:41 AM
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Replies: 1
Views: 1,330
Second hand HiSeq2500 - queries
Hi there, has anyone experienced transfer of ownership of an Illumina sequencer?
Will these work without an active service contract?
We have been offered a HiSeq2500 at a very low price...
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Forum: Sample Prep / Library Generation
08-30-2018, 10:32 AM
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Replies: 6
Views: 1,835
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Forum: Sample Prep / Library Generation
08-30-2018, 03:12 AM
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Replies: 6
Views: 1,835
Cost-effective sequencing of >200 20kb amplicons
Dear all, title says it all:
We are looking into the best/most efficient/cost effective way of fragmenting/barcoding/sequencing a ~20kb target/fragment from ~200 independent sources. Final read...
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Forum: Illumina/Solexa
12-14-2017, 05:45 AM
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Replies: 7
Views: 3,309
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Forum: Illumina/Solexa
12-14-2017, 02:16 AM
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Replies: 7
Views: 3,309
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Forum: Illumina/Solexa
12-13-2017, 07:15 AM
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Replies: 7
Views: 3,309
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Forum: Illumina/Solexa
12-13-2017, 03:26 AM
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Replies: 7
Views: 3,309
Maximum read cycles in NextSeq kits?
Hello,
We are using the 75 cycle 400M kit for paired-end sequencing.
Our understanding is that there are 75 read cycles, plus another 16 cycles (2x8 cycles) available for barcode detection. Total...
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Forum: Sample Prep / Library Generation
08-09-2016, 09:54 AM
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Replies: 18
Views: 5,376
Dear NextGenSeq, (apologies for dragging up an...
Dear NextGenSeq, (apologies for dragging up an old post!)
I have a DNA enrichment project where our inserts range from only 40bp and up. We'd like to get them all.
We've just done a run and it...
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Forum: Sample Prep / Library Generation
03-31-2016, 08:15 AM
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Replies: 48
Views: 32,192
Hi anamar,
I am pretty sure that all the...
Hi anamar,
I am pretty sure that all the Bioanalyser lanes converge into one area on the chip - at the point that they are "analysed". Each sample reaches there at different times based on the...
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Forum: Illumina/Solexa
01-27-2016, 09:47 AM
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Replies: 31
Views: 12,033
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Forum: Illumina/Solexa
01-27-2016, 09:04 AM
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Replies: 31
Views: 12,033
Info from Illumina:
The MiniSeq is similar...
Info from Illumina:
The MiniSeq is similar to the technology utilised with our NextSeq platform based on 2-channel SBS chemistry.
Pricing Information
MiniSeq System (SY-420-1001): £35,653...
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Forum: Illumina/Solexa
10-14-2015, 09:14 AM
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Replies: 6
Views: 2,573
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Forum: Illumina/Solexa
10-14-2015, 08:47 AM
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Replies: 6
Views: 2,573
Yes, we've contact tech support. They responded...
Yes, we've contact tech support. They responded last week, but nothing since...
The run is definitely below spec. When using v3 chemistry, the published specs state 2x300 should generate %Q30 >70%...
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Forum: Illumina/Solexa
10-14-2015, 12:34 AM
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Replies: 6
Views: 2,573
Here are the FWHM plots:
...
Here are the FWHM plots:
https://www.dropbox.com/s/d0k73ecj0mpfh61/Run12%20FWHM.pdf?dl=0
The bottom surface is broader and spikier - but not sure if this is a significant (meaningful)...
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Forum: Illumina/Solexa
10-07-2015, 09:31 AM
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Replies: 6
Views: 2,573
MiSeq lower quality on the bottom surface
Hello all,
Just wondering if anyone else that uses a MiSeq has observed this issue? We invariably see that the error rate and quality scores are worse on the bottom flow cell surface than the top....
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Forum: Bioinformatics
04-08-2015, 07:51 AM
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Replies: 63
Views: 9,010
Actually this is a very good point that I knew...
Actually this is a very good point that I knew about (from reading your post earlier) but recently forgot about. It turns out that part of the poor mapping of the recent run (aside from issues with...
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Forum: Bioinformatics
04-02-2015, 01:57 AM
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Replies: 63
Views: 9,010
Data in all cases is whole genome sequencing of...
Data in all cases is whole genome sequencing of S.cerevisiae genomic DNA (also containing mitochondiral DNA and an endogenous plasmid element). Prepared using NexteraXT using all standard conditions...
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Forum: Bioinformatics
04-01-2015, 08:30 AM
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Replies: 63
Views: 9,010
Hi Genomax. Actually we are really quite...
Hi Genomax. Actually we are really quite perplexed, and are starting to wonder if our last run was particularly poor quality (for as yet unknown reasons).
On the first run (3 months ago; 2x300),...
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Forum: Bioinformatics
04-01-2015, 06:43 AM
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Replies: 63
Views: 9,010
Actually I am not sure that quality drops off...
Actually I am not sure that quality drops off much at all. It appears to in the MiSeq reporter software, but this is just because so many inserts are shorter than the read length - and as Brian...
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Forum: Bioinformatics
04-01-2015, 03:56 AM
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Replies: 63
Views: 9,010
It turns out that on the last run (350+250),...
It turns out that on the last run (350+250), adapter trimming had not been enabled in MISeq. We are requeuing the analysis with Illumina so at least the output fastas will have been processed the...
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Forum: Bioinformatics
03-31-2015, 03:09 PM
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Replies: 63
Views: 9,010
As far as I know we do just run a FASTQ only on...
As far as I know we do just run a FASTQ only on the MiSeq. But my understanding was that the output sequences are already pretrimmed.
Thanks for the bbduk options explanation - I am slowly getting...
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Forum: Bioinformatics
03-31-2015, 02:11 PM
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Replies: 63
Views: 9,010
The files are correctly paired since the...
The files are correctly paired since the resulting sam files we generate clearly have pairs of reads in sequential lines that map to the same genomic location (and most of the time overlap...
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Forum: Bioinformatics
03-31-2015, 01:21 PM
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Replies: 63
Views: 9,010
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Forum: Bioinformatics
03-31-2015, 05:03 AM
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Replies: 63
Views: 9,010
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Forum: Bioinformatics
03-31-2015, 05:02 AM
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Replies: 63
Views: 9,010
We are making progress: At least in some of the...
We are making progress: At least in some of the samples, the 10% unmapped reads are coming from the 2 micron plasmid (approx 200x copies per cell it seems), and also from mitochondrial genome, which...
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