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Search: Posts Made By: 2nelly
Forum: Bioinformatics 04-20-2017, 03:18 AM
Replies: 2
Views: 1,432
Posted By 2nelly
BnaT, thank you for your answer. Yes, I...

BnaT, thank you for your answer.

Yes, I agree that using read-pair approach we can detect different alignment position of read 1 and read 2, but how do we know that translocation took place from...
Forum: Bioinformatics 04-20-2017, 02:23 AM
Replies: 2
Views: 1,432
Posted By 2nelly
translocation detection question

Hi all,

I am wondering...

how is it possible for tools like breakdancer and lumpy to detect translocations in a sample without using normal bam comparison? The reads aligned against the...
Forum: Bioinformatics 03-30-2017, 05:44 AM
Replies: 3
Views: 2,463
Posted By 2nelly
Thnx! Actually, I tried a week ago the...

Thnx!

Actually, I tried a week ago the python script for breakdancer, but this is not what I was looking for.

By the way GRanges is a good approach
Forum: Bioinformatics 03-29-2017, 02:03 AM
Replies: 3
Views: 2,463
Posted By 2nelly
SV vcf outputs to bedpe

Hi all,

Does anybody have scripts to convert:

breakdancer output ----> bedpe

delly vcf ---> bedpe

Thank you all in advance!!! cheers
Forum: Bioinformatics 03-27-2017, 02:05 AM
Replies: 1
Views: 1,408
Posted By 2nelly
How did u run MuTect using no control?Try...

How did u run MuTect using no control?Try Haplotypecaller or UnifiedGenotyper.

That way, you will discover both types germline and somatic mutations.

Then you need to filter out germline...
Forum: Bioinformatics 05-17-2016, 07:31 AM
Replies: 0
Views: 1,169
Posted By 2nelly
control-freeC error

Hi all,

I am trying to use Control-FreeC software in order to look for CNA in tumor samples, but I have to deal with an error:

terminate called after throwing an instance of 'std::bad_alloc'
...
Forum: Bioinformatics 02-23-2016, 01:51 AM
Replies: 0
Views: 1,463
Posted By 2nelly
Indelocator and Breakdancer queries

Hello to everybody,

Since i am new in the field of bioinformatics, i have 2 questions regarding 2 different softwares.

1) Does anybody could propose me the correct command to run Indelocator....
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