User: tg25

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tg250
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Posts by tg25

<prev • 7 results • page 1 of 1 • next >
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Comment: C: copy number detection from blastn results
... Thank you for your help. ...
written 12 months ago by tg250
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copy number detection from blastn results
... Hi all, Before asking this question, I looked on the internet and most of the answers that I can find deal with using lab techniques for cnv detection (which I have done for work that is not related to this question). After searching the Internet, GitHub and reading papers, I cannot find any bioi ...
next-gen blastn cnv sequencing written 12 months ago by tg250
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Comment: C: Run Delly by chromosome
... Yes, I can split the BAMs by chromosome. With doing this I have some questions: 1. If I split the BAMs then realign with bwa, would Delly detect inter chromosomal translocations? 2. Or if I split my already bwa aligned BAMs, would Delly detect inter chromosomal translocations? Before using Delly, ...
written 17 months ago by tg250
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Run Delly by chromosome
... Dear All, How do you run Delly by chromosome? I have looked at the [Delly GitHub page][1] and I cannot find the answer. I have also looked at old questions like this [Delly question][2] but this question does not address how to run by chromosome. I am running delly call -t DEL -g ref.fa -o ...
next-gen structural variant discovery delly bwa written 17 months ago by tg250
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Interpreting translocation breakpoints from BreakDancer
... Hello Everyone, I want to make sure that I am understanding the results from BreakDancer correctly when it comes to translocations. In the manual it says the following: > 1 10000 10+0- 2 20000 7+10- CTX -296 99 10 tB|10 1.00 BreakDancerMax-0.0.1 t1 With the following explanation: inter-chro ...
genome assembly next-gen breakdancer sequencing written 17 months ago by tg250
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Comment: C: Using BreakDancer output file with BreakDown
... Hello Everyone, The BreakDown program ran and completed. The output was in my .out file. 🙂 I am still learning how to use Bash along with a variety of other programs. Please, don't judge. I hope that the information in the post above helps people who want to use both BreakDancer and BreakDown. ...
written 17 months ago by tg250
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Using BreakDancer output file with BreakDown
... Hello Everyone, I am using BreakDancer for structural variant calling. I found a [BreakDancer Protocol][1] that I used to run the program on my pooled samples. At the end of this paper, in the section called Suggestions for Further Analysis there is information about another program BreakDown. In u ...
next-gen breakdancer breakdown sequencing written 17 months ago by tg250

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