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Search: Posts Made By: mavershang
Forum: Bioinformatics 12-11-2019, 12:24 PM
Replies: 0
Views: 943
Posted By mavershang
Why ref genome contains minor alleles (MAF<0.05)

Hi there, I just noticed that there are a few human variants called are actually "most dominant" in population.

For example, rs1699107, C on ref genome but its MAF=0.02

Why is this?
Forum: Bioinformatics 11-08-2016, 08:48 AM
Replies: 0
Views: 964
Posted By mavershang
Connect to miRBase and UCSC mysql database

Hi there, is there a way to directly connect to the backend database of miRBase and UCSC, and do query in code (I guess I want to know the URL, username and passwd)?

Thanks!
Forum: Bioinformatics 10-11-2016, 11:52 AM
Replies: 2
Views: 1,268
Posted By mavershang
Thanks for the suggestion. But honestly, I...

Thanks for the suggestion.

But honestly, I don't think that description page gives good guidance to start. Is there any text based page?
Forum: Bioinformatics 10-11-2016, 08:30 AM
Replies: 2
Views: 1,268
Posted By mavershang
ENCODE long-rna-seq-pipeline

Hi there. I was trying to use ENCODE long-rna-seq-pipeline to analyze miRNA-seq data (https://github.com/ENCODE-DCC/long-rna-seq-pipeline/releases/tag/v2.3.1), but got lost at the starting point: I...
Forum: Bioinformatics 06-16-2016, 01:05 PM
Replies: 0
Views: 1,916
Posted By mavershang
The miRNA pipeline used by TCGA

Hi there, I was wondering if there is any description about the pipeline to process miRNA-Seq in TCGA.

Thanks!
Forum: Bioinformatics 06-16-2016, 10:41 AM
Replies: 0
Views: 1,829
Posted By mavershang
Existing miRNA-Seq processing pipeline/tools

Hi there. I am about to start doing some miRNA-seq analysis and pipeline development.

Could anyone give me some suggestions on the existing tools/pipelines I could use?

Thanks!
Forum: Bioinformatics 05-12-2015, 09:06 AM
Replies: 1
Views: 1,532
Posted By mavershang
How to add CADD score to variant annotation using dbNSFP

Hi there,

I want to add CADD for the variant annotation, and easily directed to dbNSFP. According to its official site (https://sites.google.com/site/jpopgen/dbNSFP), dbNSFP has integrated CADD.
...
Forum: Bioinformatics 05-12-2015, 07:54 AM
Replies: 0
Views: 876
Posted By mavershang
Calculating coverage for regions with at least 1X for every nucleotide

Hi there, I have some WES samples been mapped.

Without using the manufacture interval BED file, I am wondering if there is any way to calculate the coverage for each region (not necessarily...
Forum: Bioinformatics 12-05-2014, 06:22 AM
Replies: 0
Views: 1,244
Posted By mavershang
Questions running Delly to detect copy number variation

Hi there. I am running delly to detect CNV.

There are 6 BAM I need to run. Is there any difference if I run it like

delly -t DUP -o sample1.out -g ref.fa sample1.bam
delly -t DUP -o...
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