Forum: Sample Prep / Library Generation
11-28-2016, 02:02 AM
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Replies: 5
Views: 2,069
% of duplicates per gene
One thing I've looked at is the % of duplicates per gene. If you have a high number of duplicates only in a few genes you should be fine, but if you have low expression genes with high duplication...
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Forum: Bioinformatics
11-21-2016, 08:57 AM
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Replies: 6
Views: 12,938
Another alternative
For RNA seq data (which has intron spanning reads) I made the following script which:
1. Does not report coverage over introns.
2. Generates one file for each strand
3. Summarized data in 10 bp...
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Forum: Sample Prep / Library Generation
02-03-2016, 01:21 PM
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Replies: 17
Views: 9,919
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Forum: Bioinformatics
12-07-2015, 04:36 AM
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Replies: 15
Views: 11,968
What about cross batch comparison
We have recently added a 300 sample library with ERCC controls. The idea behind this is that these are part of large scale study which will happen over time. This means that we cannot be certain that...
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Forum: Epigenetics
07-06-2015, 02:27 AM
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Replies: 5
Views: 8,018
Nextera MeDip !!! hell yeah
this sounds like the best option for me??? Did you try it out I would like to try it as well (I'm a big Nextera fan)!!! I read somewhere else that Illumina primers can be methylated sometimes, but...
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Forum: Ion Torrent
04-21-2015, 08:50 AM
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Replies: 122
Views: 112,903
Updates on Illumina vs IonTorrent
a must read: http://omicsomics.blogspot.se/2015/02/can-ion-torrent-buzz-again.html
I have to agree with Keith here, I would love to hear some company giving Illumina a run for their money. The...
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Forum: Ion Torrent
01-27-2015, 07:56 AM
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Replies: 122
Views: 112,903
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Forum: Ion Torrent
01-21-2015, 09:14 AM
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Replies: 122
Views: 112,903
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Forum: Bioinformatics
08-28-2013, 06:50 AM
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Replies: 13
Views: 9,208
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Forum: Bioinformatics
08-28-2013, 12:39 AM
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Replies: 13
Views: 9,208
still same problem with column not found...
I have the same problem with fastq-dump.2.3.2,
column not found while opening table within short read archive module
tried -A, the perl configuration, the jar, nothing seems to work??
I'm...
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Forum: Ion Torrent
04-18-2013, 08:34 AM
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Replies: 70
Views: 23,072
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Forum: Illumina/Solexa
04-15-2013, 10:35 AM
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Replies: 2
Views: 1,352
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Forum: Illumina/Solexa
04-15-2013, 02:47 AM
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Replies: 2
Views: 1,352
Miseq ReagentValve
13-04-13 13:58:33.872 +01 000000017 INF: Selector valve "ReagentValve" timed out on attempt #1: "ReagentValve: '+08\r' command timed out waiting 60000/60000 ms for any of "'*','\r'"; received ''
...
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Forum: Illumina/Solexa
03-08-2013, 07:09 AM
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Replies: 20
Views: 22,847
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Forum: Ion Torrent
02-24-2013, 03:39 AM
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Replies: 70
Views: 23,072
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Forum: Ion Torrent
02-24-2013, 03:08 AM
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Replies: 70
Views: 23,072
Let me first confess that I know I have no idea...
Let me first confess that I know I have no idea how to run a company, but engaging in these conversations even if I get a bashing like the one on top are really good learning experience. I want to...
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Forum: Ion Torrent
02-18-2013, 01:15 AM
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Replies: 70
Views: 23,072
No I'm not sure who Dr Collins is, I'm just a...
No I'm not sure who Dr Collins is, I'm just a bioinformatics phd student (with delusions of business).
Well, there is no real reason why you should have flying cars (you can still make lots of...
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Forum: Ion Torrent
02-17-2013, 08:48 AM
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Replies: 70
Views: 23,072
The question is: You go to the doctor for some...
The question is: You go to the doctor for some condition and before prescribing a particular medicine he swabs your mouth and puts it into his Pfizer subsidiced desktop genome analyzer which reads...
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Forum: Ion Torrent
02-14-2013, 02:01 AM
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Replies: 70
Views: 23,072
P.S: In retrospect, the MiSeq was the best...
P.S: In retrospect, the MiSeq was the best choice, and still is the best choice for us. Had we bought the PGM we would be in a world of hurt as we have heard how people struggle with sample prep. Our...
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Forum: Ion Torrent
02-14-2013, 01:54 AM
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Replies: 70
Views: 23,072
Betamax vs VHS???
Any updates on the contest, is Ion keeping up with the PII promise? I keep hearing about people buying MiSeqs/HiSeqs here in Sweden but I have yet to see a IonProton? It feels as if Ion needs the PII...
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Forum: Illumina/Solexa
07-11-2012, 08:16 AM
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Replies: 12
Views: 4,373
well even if they are flitered out, it will...
well even if they are flitered out, it will introduce a heck of a lot of N's in a large number of reads, not sure how big that pic is but the blob is on top of a lot of clusters. Why only C, well I...
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Forum: Illumina/Solexa
07-10-2012, 12:03 PM
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Replies: 12
Views: 4,373
Yeap, I've been looking at the raw files and I...
Yeap, I've been looking at the raw files and I see these "blobs" / "flares" all the time, where do they come from?
On the other hand, I think we could be having a problem with adapter dimers, we...
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Forum: Illumina/Solexa
07-10-2012, 11:31 AM
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Replies: 12
Views: 4,373
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Forum: Illumina/Solexa
07-10-2012, 11:21 AM
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Replies: 12
Views: 4,373
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Forum: Illumina/Solexa
05-31-2012, 09:12 AM
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Replies: 17
Views: 11,755
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