User: maduh17

gravatar for maduh17
maduh1710
Reputation:
10
Status:
New User
Location:
Kuala Lumpur, Malaysia
Last seen:
7 months, 1 week ago
Joined:
1 year, 8 months 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 >
0
votes
2
answers
2.3k
views
2
answers
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 9 months ago by maduh1710
0
votes
0
answers
219
views
0
answers
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 9 months ago by maduh1710
0
votes
5
answers
3.2k
views
5
answers
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 9 months ago by maduh1710
0
votes
2
answers
1.2k
views
2
answers
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 10 months ago by maduh1710
0
votes
2
answers
380
views
2
answers
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 11 months ago by maduh1710
0
votes
3
answers
11k
views
3
answers
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 11 months ago by maduh1710
0
votes
1
answer
890
views
1
answers
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 12 months ago by maduh1710
0
votes
0
answers
582
views
0
answers
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 12 months ago by maduh1710
0
votes
0
answers
532
views
0
answers
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 13 months ago by maduh1710 • updated 13 months ago by WouterDeCoster34k
0
votes
6
answers
2.2k
views
6
answers
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 15 months ago by maduh1710

Latest awards to maduh17

Autobiographer 12 months ago, has more than 80 characters in the information field of the user's profile.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 672 users visited in the last hour