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Forum: Sample Prep / Library Generation 11-28-2016, 01:02 AM
Replies: 5
Views: 1,793
Posted By aleferna
% 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...
Forum: Bioinformatics 11-21-2016, 07:57 AM
Replies: 6
Views: 10,815
Posted By aleferna
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...
Forum: Sample Prep / Library Generation 02-03-2016, 12:21 PM
Replies: 17
Views: 8,988
Posted By aleferna
never got a answer for this, so what is better...

never got a answer for this, so what is better Covaris or the chemical/heat fragmentation? ?
Forum: Bioinformatics 12-07-2015, 03:36 AM
Replies: 15
Views: 9,936
Posted By aleferna
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...
Forum: Epigenetics 07-06-2015, 01:27 AM
Replies: 5
Views: 7,565
Posted By aleferna
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...
Forum: Ion Torrent 04-21-2015, 07:50 AM
Replies: 121
Views: 104,776
Posted By aleferna
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...
Forum: Ion Torrent 01-27-2015, 06:56 AM
Replies: 121
Views: 104,776
Posted By aleferna
We bought the MiSeq when the PGM came out and was...

We bought the MiSeq when the PGM came out and was still comparable with the MiSeq. I don't know about Ion, but it seems the MiSeq simply works... consistently and as advertised. I've read in other...
Forum: Ion Torrent 01-21-2015, 08:14 AM
Replies: 121
Views: 104,776
Posted By aleferna
Is there any updated comparisons between the...

Is there any updated comparisons between the Proton and the MiSeq?
Forum: Bioinformatics 08-28-2013, 05:50 AM
Replies: 13
Views: 8,504
Posted By aleferna
Yeap tried wiht the full path, when I do this the...

Yeap tried wiht the full path, when I do this the error message changes from file not found to the problem with the columns?
Forum: Bioinformatics 08-27-2013, 11:39 PM
Replies: 13
Views: 8,504
Posted By aleferna
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...
Forum: Ion Torrent 04-18-2013, 07:34 AM
Replies: 70
Views: 20,336
Posted By aleferna
I also don't understand the comparison between...

I also don't understand the comparison between the Proton and the Miseq? Isn't Proton at the HiSeq 1000 price segment? Have the prices changed, I though after server, extra stuff the...
Forum: Illumina/Solexa 04-15-2013, 09:35 AM
Replies: 2
Views: 1,203
Posted By aleferna
yeap, but I'm not sure if we ever did get the...

yeap, but I'm not sure if we ever did get the valve replaced.. I remember the tech mentioned something about replacing it, but I'm not sure if he finally did replace it.
Forum: Illumina/Solexa 04-15-2013, 01:47 AM
Replies: 2
Views: 1,203
Posted By aleferna
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 ''

...
Forum: Illumina/Solexa 03-08-2013, 06:09 AM
Replies: 20
Views: 20,789
Posted By aleferna
I have the same problem here

I have the same problem here
Forum: Ion Torrent 02-24-2013, 02:39 AM
Replies: 70
Views: 20,336
Posted By aleferna
Well, I would revise the traction of NGS if the...

Well, I would revise the traction of NGS if the price goes down to $100, old ideas are not necessarily bad. Turing had very bad decade old ideas that didn't get traction.

The stock market is...
Forum: Ion Torrent 02-24-2013, 02:08 AM
Replies: 70
Views: 20,336
Posted By aleferna
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...
Forum: Ion Torrent 02-18-2013, 12:15 AM
Replies: 70
Views: 20,336
Posted By aleferna
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...
Forum: Ion Torrent 02-17-2013, 07:48 AM
Replies: 70
Views: 20,336
Posted By aleferna
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...
Forum: Ion Torrent 02-14-2013, 01:01 AM
Replies: 70
Views: 20,336
Posted By aleferna
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...
Forum: Ion Torrent 02-14-2013, 12:54 AM
Replies: 70
Views: 20,336
Posted By aleferna
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...
Forum: Illumina/Solexa 07-11-2012, 07:16 AM
Replies: 12
Views: 3,683
Posted By aleferna
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...
Forum: Illumina/Solexa 07-10-2012, 11:03 AM
Replies: 12
Views: 3,683
Posted By aleferna
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...
Forum: Illumina/Solexa 07-10-2012, 10:31 AM
Replies: 12
Views: 3,683
Posted By aleferna
Even more so I'm getting these weird effects

Even more so I'm getting these weird effects
Forum: Illumina/Solexa 07-10-2012, 10:21 AM
Replies: 12
Views: 3,683
Posted By aleferna
Any progress on these I'm getting the same...

Any progress on these I'm getting the same problem?
Forum: Illumina/Solexa 05-31-2012, 08:12 AM
Replies: 17
Views: 11,198
Posted By aleferna
Well I guess we can allways sue them... I mean it...

Well I guess we can allways sue them... I mean it was in the tender for our machine
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