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Forum: Bioinformatics 05-31-2014, 08:44 AM
Replies: 0
Views: 1,367
Posted By choijae3
bwa-mem -M parameter and SV detection software compatability

I wanted to ask people with experience using bwa mem to align their reads and use the bam file to detect SVs using programs such as pindel, breakdancer, CNVnator, svdetect.

I know that the -M...
Forum: Bioinformatics 05-20-2014, 05:34 AM
Replies: 0
Views: 913
Posted By choijae3
cnvnator visualizing result with root

Hi everyone

I had a quick question with looking at the region of interest predicted by cnvnator on root.
I was curious on how and what exactly is being plotted on root.
I've indicated a bin_size...
Forum: Bioinformatics 05-06-2014, 02:06 PM
Replies: 0
Views: 746
Posted By choijae3
Pindel predicts inversions using only one side of the anchors

Hi folks

I have a somewhat unique problem to detect SV (especially inversions) using PE data. I've been using pindel to detect SV. Without going too much in detail of my genome of interest it's a...
Forum: Sample Prep / Library Generation 03-19-2014, 02:52 PM
Replies: 0
Views: 1,219
Posted By choijae3
rRNA & tRNA contamination in whole genome sequencing

Hi folks

I had a peculiar phenomenon happening with my genome reqsequencing project and was wondering if other people have seen this.

I've been using Qiagen's DNeasy kit to isolate Drosophila...
Forum: Bioinformatics 01-08-2014, 07:27 AM
Replies: 5
Views: 2,676
Posted By choijae3
Hi barkasn thanks for the reply! I've been...

Hi barkasn

thanks for the reply! I've been following best practice from broad institute and have done the mark duplicate steps. I haven't paid much attention to it (I really should have) and found...
Forum: Bioinformatics 01-07-2014, 02:22 PM
Replies: 5
Views: 2,676
Posted By choijae3
Yes I should have ment multiplexing instead of...

Yes I should have ment multiplexing instead of pooling. I'm conducting a population genomic type project and trying to sequence as much populations without sacrificing coverage too much.

Thanks...
Forum: Bioinformatics 01-07-2014, 01:45 PM
Replies: 5
Views: 2,676
Posted By choijae3
nvm so I've found useful links to solve my...

nvm so I've found useful links to solve my problem from here (http://www.biostars.org/p/6544/) and here (http://seqanswers.com/forums/showthread.php?t=12070)

however is my approach makes sense in...
Forum: Bioinformatics 01-07-2014, 01:36 PM
Replies: 5
Views: 2,676
Posted By choijae3
How to randomly remove portions of the raw reads from the FASTQ file

Hi everyone

I'm a graduate student just started to do some NGS for my thesis project.

Most of the problems I had I could have searched and found it here on seq answer but I think I have a...
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