User: ahmad.moousavi

Reputation:
40
Status:
New User
Location:
Royan Institute, Tehran, Iran
Last seen:
22 hours ago
Joined:
2 years, 1 month ago
Email:
a*************@gmail.com

Posts by ahmad.moousavi

<prev • 20 results • page 1 of 2 • next >
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Comment: C: What are the best tools for visualizing DNA methylation result?
... Dear Antonio, Thank you so much. I have used CGmaptools and methgo, but during running **methgo met** function I have got this error, do you have any idea about that? Thanks. Traceback (most recent call last): File "/home/gen/apps/methgo/methgo", line 13, in module.main() ...
written 13 days ago by ahmad.moousavi40
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What are the best tools for visualizing DNA methylation result?
... Hi I have analyzed RRBS data, in this phase I look for good tool for visualizing genomic position of DMRs. What tool you suggest for visualizing methylation result based on bed file or coverage file made by Bismark? I wanted to create figure contains methylation position along with TSS, Promoter ...
methylation rrbs rna-seq written 29 days ago by ahmad.moousavi40 • updated 27 days ago by Antonio R. Franco3.7k
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Comment: C: How to interepret DNA methylation by DSS package?
... Thanks dear Devon, I couldn't find good manual for that. My problem is how to infer high/low methylated values, it might be false idea to compare this result with RNA-SEQ but how average methylation is calculated ? is this mean from for example meanMethyl1: 34 % of 38 CGs were methylated? And when ...
written 5 weeks ago by ahmad.moousavi40
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How to interepret DNA methylation by DSS package?
... Hi everyone, I have done RRBS analysis by DSS package, it gave differentially methylated regions (DMR) with some strange value, based on manual and author's information. I have got significant result. I have two questions: 1- I have got ~50.000 DMR (siginicant) in each comparison, is it normal? 2- ...
rrbs wgbs written 5 weeks ago by ahmad.moousavi40 • updated 5 weeks ago by Devon Ryan81k
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Comment: C: Problem with annovar in GATK4 output
... thanks for reply. The problems still exist. I have 5 sample ( output from Haplotypecaller which merged by Bcftools), but after running you command each file is separated and it is hard to track a SNP in all 5 samples. Can I annotate all 5 samples individually and then merge annotated result into o ...
written 3 months ago by ahmad.moousavi40
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Comment: C: Easy way to do GO enrichment in R
... just paste your gene in enrichR website; in R you could input your genes as a vector in below code : enriched <- enrichr(genes8000, dbs) ...
written 4 months ago by ahmad.moousavi40
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Problem with annovar in GATK4 output
... Hello Based on GATK4 best practices pipline I have made a VCF file composed 4 person WES data. When I want to annotate it with annovar , **but annovar could not annotate all variations and near 70% of variations discard and gone to Invalid_input.** I though it might happen due to VCF version (4.2) ...
exome gatk4 annovar written 4 months ago by ahmad.moousavi40
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Using gVCF mode in HaplotypeCaller ( GATK4)
... Hi I have problem in using HaplotypeCaller gVCF mode ( GATK4 best practices). Please let me know following problems: 1- Should we run gVCF even when we have one WES sample? 2- I have 3 WES samples, should I use gVCF --> Cosolidate --> GenotypeGVCF --> VCF or it is better to obtain VCF d ...
gatk4 haplotypecaller snp written 5 months ago by ahmad.moousavi40 • updated 5 months ago by JJ320
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How to do DMR analysis with BiSeq (for RRBS methylation data)?
... Hi I have **20 RRBS samples** which I wanted to do do deferentially methylated region (DMR) analysis with BiSeq or other R packages, however the manual resource is not enough. I want to do DMR analysis on all chromosomes not specific regions. Is there anybody who has experience with BiSeq: ...
methylation dmr sequencing written 6 months ago by ahmad.moousavi40
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Error in methylKit in DMR analysis
... Hi I have 20 (RRBS) samples in 7 groups and it gives below error for clusterSamples: I have got a problem when I run methylkit on Bismark .cov output files, my code : meth <- unite(myobj, destrand=FALSE) getCorrelation(meth,plot=TRUE) clusterSamples(meth, dist="correlation", method= ...
rrbs wgbs written 6 months ago by ahmad.moousavi40

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Popular Question 24 days ago, created a question with more than 1,000 views. For Easy way to do GO enrichment in R

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