Forum: General
01-01-2018, 07:49 PM
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Replies: 2
Views: 1,640
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Forum: General
12-31-2017, 09:54 AM
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Replies: 2
Views: 1,640
What is the current state of sequencing?
Hey all,
It's been several years since I last logged in and several years since I've been involved in sequencing. I'm curious how things have progressed in the last handful of years. Is there any...
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Forum: Bioinformatics
11-17-2013, 03:14 PM
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Replies: 3
Views: 1,870
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Forum: Bioinformatics
11-05-2013, 07:31 AM
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Replies: 15
Views: 2,281
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Forum: Sample Prep / Library Generation
11-04-2013, 04:56 PM
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Replies: 3
Views: 4,071
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Forum: Bioinformatics
10-28-2013, 09:40 AM
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Replies: 3
Views: 2,228
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Forum: General
10-15-2013, 07:14 AM
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Replies: 4
Views: 2,699
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Forum: General
10-14-2013, 08:34 PM
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Replies: 4
Views: 2,699
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Forum: Bioinformatics
09-08-2013, 07:51 PM
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Replies: 4
Views: 2,004
What book are you reading and what year was it...
What book are you reading and what year was it published? That is not an accurate statement, I don't think. The bottlenecks are usually either obtaining relevant clinical samples, obtaining sequence...
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Forum: Introductions
09-06-2013, 06:15 PM
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Replies: 5
Views: 3,085
You didn't really ask a question. What exactly...
You didn't really ask a question. What exactly does your lab work on that would justify using RNA-seq? In terms of showing nice data I imagine you can use things already published and show how...
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Forum: Bioinformatics
08-28-2013, 05:16 PM
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Replies: 1
Views: 3,822
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Forum: Bioinformatics
08-25-2013, 06:00 PM
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Replies: 2
Views: 1,712
I haven't used it in forever but it may be...
I haven't used it in forever but it may be keeping the old quality scores as well as the recalibrated ones. If that is default now there is an option to have it not do that (at least there was over a...
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Forum: Genomic Resequencing
08-20-2013, 10:57 AM
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Replies: 3
Views: 3,361
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Forum: Bioinformatics
08-19-2013, 09:42 AM
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Replies: 16
Views: 14,917
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Forum: Bioinformatics
08-11-2013, 07:41 PM
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Replies: 12
Views: 12,913
I think your next step is to try to figure out...
I think your next step is to try to figure out what's going on. I'd start with W1 and W2 as they seem to be horribly correlated but should be biological replicates.
So I would do a few things with...
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Forum: Bioinformatics
08-10-2013, 07:12 AM
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Replies: 5
Views: 1,397
I have not used Somaticsniper, but many callers...
I have not used Somaticsniper, but many callers will allow you to specify a list of regions for which to call SNVs. Read through the manual perhaps and see if that's allowed. Otherwise, it depends on...
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Forum: Bioinformatics
08-06-2013, 10:51 PM
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Replies: 12
Views: 12,913
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Forum: Bioinformatics
08-06-2013, 10:00 AM
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Replies: 4
Views: 2,157
Maybe others will have ideas, but if they are...
Maybe others will have ideas, but if they are exactly the same (ie, identical headers, bases, quality scores), you could convert them to one line, combine the files, sort them, and then use uniq, as...
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Forum: General
08-04-2013, 08:10 PM
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Replies: 4
Views: 8,085
Thank you, I'm a new python user. School is...
Thank you, I'm a new python user. School is starting up for me tomorrow so it'll be a bit before I can look at this in more detail but I will do so within a week. Thank you very much for the feedback.
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Forum: General
08-04-2013, 02:52 PM
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Replies: 5
Views: 1,897
If you google you may find this link:...
If you google you may find this link: http://unix.stackexchange.com/questions/18736/how-to-count-the-number-of-a-specific-character-in-each-line
Here's a bash script that will work. Run it as...
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Forum: General
08-04-2013, 02:27 PM
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Replies: 4
Views: 8,085
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Forum: General
08-04-2013, 09:33 AM
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Replies: 4
Views: 8,085
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Forum: Bioinformatics
08-02-2013, 07:33 AM
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Replies: 9
Views: 2,019
As mastal said, you should; that's what I was...
As mastal said, you should; that's what I was alluding to above. Could you specify your restriction footprint as part of your adapter sequence? Would the footprint always be the same? If so that can...
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Forum: Bioinformatics
08-01-2013, 12:08 PM
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Replies: 6
Views: 3,835
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Forum: Bioinformatics
08-01-2013, 08:44 AM
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Replies: 9
Views: 2,019
I don't know if you're willing to re-analyze...
I don't know if you're willing to re-analyze everything, but if you are you can specify cut adapt to get rid of reads that are 6bp or shorter. But again, if you have paired end reads you need to be...
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