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Forum: Bioinformatics 04-20-2017, 03:02 AM
Replies: 2
Views: 1,481
Posted By BnaT
Hello, BreakDancer, Lumpy and many others...

Hello,

BreakDancer, Lumpy and many others are based on the clustering of discordant signals from mapping to the reference genome. In the case of translocations, any read-pair supporting it might...
Forum: RNA Sequencing 12-05-2016, 05:27 AM
Replies: 5
Views: 19,332
Posted By BnaT
If you only need to check a single read or a few,...

If you only need to check a single read or a few, you could use BLAST. Otherwise, you could try bwa-mem with -a option to get the secondary alignments. Also you could try GEM-mapper which in default...
Forum: Bioinformatics 11-14-2016, 04:42 AM
Replies: 2
Views: 1,400
Posted By BnaT
There's a wide variety of SV callers that support...

There's a wide variety of SV callers that support inversion calling. I'd suggest DELLY or Pindel, they do well with inversions and are simple to use.
Forum: Bioinformatics 08-30-2016, 06:11 AM
Replies: 3
Views: 1,652
Posted By BnaT
There are a few algorithms available, I'd try...

There are a few algorithms available, I'd try Socrates (split-read) which works either on PE or SE data.
http://bioinf.wehi.edu.au/socrates/
Forum: Oxford Nanopore 05-24-2016, 06:51 AM
Replies: 0
Views: 1,673
Posted By BnaT
SV using nanopore

Hi, I am very excited with this technology, and I was thinking in detecting breakpoints from a bunch of samples in which I found some CNVs. We did targeted sequencing so it was impossible to resolve...
Forum: Bioinformatics 11-03-2015, 12:40 AM
Replies: 0
Views: 855
Posted By BnaT
CNV calling with BWA mem

Hi,

In my center we are interested in calling CNVs from targeted resequencing using Illumina's MiSeq and I am facing the following issue:

Two of the regions of interest share high homology,...
Forum: Bioinformatics 05-20-2015, 03:44 AM
Replies: 3
Views: 1,156
Posted By BnaT
I'd try filtering with FLAG 0x100 or 256....

I'd try filtering with FLAG 0x100 or 256. Sometimes I have seen inconsistencies depending on the mapper being used (e.g GEM mapper).
Forum: Bioinformatics 12-18-2014, 05:42 AM
Replies: 0
Views: 1,096
Posted By BnaT
Soft-clipping resequencing panel

Hello guys,
I have some issues to understand the soft-clipped reads. I am analyzing a targeted resequencing panel. I trimmed the FASTQs, but I found very few trimmed bases. From a bam file, I have...
Forum: Bioinformatics 11-26-2014, 05:48 AM
Replies: 0
Views: 689
Posted By BnaT
Anomalous paired-end reads from a resequencing project

Hi guys, I'm analysing some samples from a resequencing project.
After mapping (BWA-mem) and removing duplicates I've found a background of anomalous paired-end reads mapping to almost every exon:...
Forum: Bioinformatics 11-12-2014, 04:05 AM
Replies: 1
Views: 979
Posted By BnaT
Insert size distribution for SV detection

I'm new to bioinformatic analysis and statistics, and this is my first post.
I've got a basic question regarding the insert size distribution of paired-end reads.
Most of PEM-based SV callers...
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