User: maduh17

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maduh1710
Reputation:
10
Status:
New User
Location:
Kuala Lumpur, Malaysia
Last seen:
1 day, 8 hours ago
Joined:
11 months, 1 week ago
Email:
m******@gmail.com

Wet lab scientist turned dry lab programmer.

BSc in Biochemistry, PhD in computational biology on core promoters and enhancers in flies.

Currently working on whole exome sequencing in humans!

Posts by maduh17

<prev • 12 results • page 1 of 2 • next >
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Answer: A: mutation signature in cancer
... Awesome, I was just going to ask a similar question! Rather not write the code from the Methods by the original paper by Alexandrov! ...
written 3 days ago by maduh1710
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High CG>CA and CG>TG errors from bait bias WES
... Hi there, I've ran picard's CollectSequencingArtifactMetrics on my WES samples, both on my fresh-frozen tumors and blood normals. **In trinucleotide context, I'm seeing high "bait bias" errors CG>CA and CG>TG in both tumors and normals.** These two error types cluster separately from other t ...
wes bias written 4 days ago by maduh1710
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Answer: A: Remove positions that are non-variant in a subset of samples from a vcf file
... You can also use `awk`, but be careful which columns: cat raw_variants.vcf | \ awk '($0~/^#/)($0!~/^#/){split($10,x,":"); if(x[1]!="0/0") print }' > hard_filtered.vcf ...
written 11 days ago by maduh1710
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Answer: A: Vcf-compare two multi-sample vcf files
... !!!!!!!!!!!!!!!!! I found a link saying that **GATK's** GenotypeConcordance is being outphased: https://gatkforums.broadinstitute.org/gatk/discussion/5795/genotype-concordance-output **So might wanna just use picard as Pierre suggested** ...
written 6 weeks ago by maduh1710
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Answer: A: How to calculate copies of circulating tumour DNA from sequencing data?
... I recently looked around for methods to determine copy number aberration (CNA) using shallow whole genome sequencing (sWGS) and came across this paper: https://www.ncbi.nlm.nih.gov/pubmed/28710315 But that's all I know. I've running sWGS to detect CNAs at ~0.05X from tumor samples (not from blood ...
written 12 weeks ago by maduh1710
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Answer: A: Shallow Sequencing Vs Deep Sequencing
... To determine copy number variation, it is enough to do "shallow" whole genome sequencing, at 0.1-0.2X coverage. To confidently call mutation in heterogenous population of cells, for example in cancer, you might want to go for "deeper" coverage, at 80X or higher. For relatively homogenous cells su ...
written 3 months ago by maduh1710
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Answer: A: How to set the GATK_PATH of PolySolver
... It seems that the software is ridden with many issues. I'm also right now struggling with installation + fixing broken links + fixing file extensions that are missing in the scripts etc. The email provided at the website bounced my email back. ...
written 3 months ago by maduh1710
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Comment: C: Cannot install ATHLATES, issues with bamtools
... I'm also having the same problem. I even changed the line `#include "api/BamReader.h"` in the `src/bam_manip.h` file to the correct path of BamReader.h of bamtools. Still doesn't work. It still says it can't find `api/BamReader.h` ...
written 3 months ago by maduh1710
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Nextera Rapid Capture Exome Regions hg38
... Hi everyone, Has anyone worked with Nextera Rapid Capture WES on hg38 assembly? Illumina has only hg19 targeted regions as a bed file on their website. I'm wondering anyone has a lifted-over file and thoroughly checked it's all fine. Many thanks. Mamduh ...
exome assembly nextera written 4 months ago by maduh1710 • updated 4 months ago by WouterDeCoster26k
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Answer: A: Bioinformatics and wet lab science combined
... If you really want to extremely good at one of the things you'd need to concentrate fully on that thing. Being extremely good at computational biology is worth it. But make sure you are willing to do the necessary sacrifice, and you like it. ...
written 6 months ago by maduh1710

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