User: devarora

gravatar for devarora
devarora240
Reputation:
240
Status:
Trusted
Location:
SouthKorea
Scholar ID:
Google Scholar Page
Last seen:
13 hours ago
Joined:
2 years, 10 months ago
Email:
d*******@hotmail.com

So many questions

In brief..looking for answers..!!

Currently, I am working with RNAseq, WGS, WGBS data and integration analysis.

My top strengths are teamwork, time management, and analytical skills with willingness to work on different projects. 

I love Python and R programming and Improving my skills.

Posts by devarora

<prev • 116 results • page 1 of 12 • next >
0
votes
0
answers
77
views
0
answers
Methylation data analysis
... I am trying to compare tissue specific methylation analysis and mapped methylated region to CpG island coordinates. Now, we found few identified genes are methylated and over-expressed. My understanding and existing literature suggest that methylation at CpG island leads to decrease in gene expressi ...
gene wgbs rna-seq cpg written 8 days ago by devarora240
0
votes
1
answer
78
views
1
answers
Answer: A: Plotting the results (p-values) from various conditional GWAS
... I believe there are different ways to represent significant results but I found circos in highlighting region of interest as one of the most interactive way as well as Manhattan plot for the same. I found these particular tools with well documented example and help forum to proceed in my work. [Ci ...
written 11 days ago by devarora240
0
votes
2
answers
100
views
2
answers
Answer: A: circos error - no change to housekeeping.conf
... Valid point by @mbk0asis. Why not reduce the size by either increasing binsize or use some filter in your data otherwise there will be noise all over the chromosome. Although you can get the output by looking into etc folder (most probably) and just change the parameter in housekeeping.conf file ...
written 23 days ago by devarora240
0
votes
1
answer
139
views
1
answers
Answer: C: Missing chromosomal Information after sorting and deduplication step
... There is an update in the following issue. I have contacted the developer and he found that within R these numbers were represented with scientific notation, like 2176+e1 for 2176_0_ or 2176+e2 for 2176_00_, and when we exported to bed/txt format the notation was not respected. ...
written 7 weeks ago by devarora240
1
vote
1
answer
150
views
1
answer
Bismark methylation extract result interpretation
... I have identified DEGs and interested to know methylation effect if so during evolution. We performed WGBS sequencing and extracted gene of interest and performed bismark methyl extract to the output specific region BAM file. I have attached the output but confused why it shows CpG methylation over ...
methylation wgbs bismark cpg written 9 weeks ago by devarora240 • updated 9 weeks ago by Ventrilocus80
0
votes
1
answer
139
views
1
answers
Comment: C: Missing chromosomal Information after sorting and deduplication step
... Yes, a number is missing in the end. I checked in BAM file for one position and found the last digit was "0" which was missing. Similarly, there are many missing value. This output was generated by previous colleague and I have limited understanding. From the data I able to know this was methyl call ...
written 9 weeks ago by devarora240
0
votes
1
answer
139
views
1
answers
Comment: C: Missing chromosomal Information after sorting and deduplication step
... Respected Sir/Mam, I received the data already preprocessed. The sorting and deduplication was performed on BAM file after QC and mapping. I found strange results and have no lead what could have happened and what leads to certain missing information. ...
written 9 weeks ago by devarora240
0
votes
1
answer
139
views
1
answer
Missing chromosomal Information after sorting and deduplication step
... I am working on methylated data and found such issue where position is not mapped completely. May I know if someone encountered such data and how to fix. Here 2176 should be 2176X and this is all over the cromosome. chr, start, end, strand "1", 20850, 20850, "+" "1", 20944, 20944, "+" "1", 21128 ...
assembly next-gen sequence methylation written 9 weeks ago by devarora240
0
votes
0
answers
198
views
0
answers
Comment: C: Post GWAS mapping SNPs to genes and calculating p-values
... I believe you first have to map snps to the gene (See VEP or BioMart) and than use vlookup to get corresponding p-values. ...
written 10 weeks ago by devarora240
0
votes
2
answers
847
views
2
answers
Answer: A: Creating assembly graphs .gfa
... Yes, by [SibeliaZ][1] you can get .gfa file out of a fasta file. They recently updated there old version and now large genome file can also be used for the same. [1]: https://github.com/medvedevgroup/SibeliaZ ...
written 10 weeks ago by devarora240

Latest awards to devarora

Centurion 3 months ago, created 100 posts.
Autobiographer 9 months ago, has more than 80 characters in the information field of the user's profile.
Supporter 10 months ago, voted at least 25 times.
Scholar 10 months ago, created an answer that has been accepted. For A: How to do chromosome painting?
Scholar 10 months ago, created an answer that has been accepted. For A: How to do chromosome painting?
Scholar 11 months ago, created an answer that has been accepted. For A: How to do chromosome painting?
Scholar 12 months ago, created an answer that has been accepted. For A: How to do chromosome painting?
Popular Question 12 months ago, created a question with more than 1,000 views. For WGCNA TOM calculation time

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1316 users visited in the last hour