User: mavershang

gravatar for mavershang
mavershang50
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50
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Trusted
Location:
United States
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2 weeks, 4 days ago
Joined:
5 years, 10 months ago
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m*********@gmail.com

Posts by mavershang

<prev • 14 results • page 1 of 2 • next >
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Comment: C: NCBI E-utilities API function esearch not working
... Thank you. I misinterpret it. The error is actually due to the default SSL/TLS protocolType change in my code. Now it's working. ...
written 18 days ago by mavershang50
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Comment: C: NCBI E-utilities API function esearch not working
... For example, this url display the full xml > https://www.ncbi.nlm.nih.gov/sra/ERX2021050[accn]?report=FullXml Esearch used to return the same xml. ...
written 18 days ago by mavershang50
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Comment: C: NCBI E-utilities API function esearch not working
... This is actually what I get and it doesn't have any style information. It suppose to have much more fields ...
written 18 days ago by mavershang50
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NCBI E-utilities API function esearch not working
... Hi there. I have a old code to retrieve xml of a SRX using NCBI E-utilities API. For example, using the url as below (you can remove api_key part) https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=sra&retmax=10000&term=ERX2021050&api_key=blablablabla I am pretty sure it wor ...
ncbi written 18 days ago by mavershang50 • updated 18 days ago by Pierre Lindenbaum131k
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Suggestions on miRNA analysis tools/pipeline
... Hi there, I just started to do miRNA-Seq analysis. After doing some homework, I got very basic ideas about some tools/pipeline could be used (lke miRDeep2, miRAnalyzer, CAP-miRNA, etc). Do you guys have any suggestions on the performance and reliability of these tools/pipeline (or maybe some other ...
rna-seq written 4.4 years ago by mavershang50 • updated 4.4 years ago by JohnBlue81300
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How to check the reads coverage of an area in ExAC, ESP6500, and 1000Genomes
... Hi there, I want to check the reads coverage of several areas in ExAC, ESP6500, and 1000Genomes. Does these public DB provide DP/nt or similar data? Thanks! ...
next-gen written 5.1 years ago by mavershang50 • updated 5.1 years ago by Vivek2.4k
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Comment: C: Convert Indel format in vcf
... The program failed with error "core dump". So finally I wrote my own code to solve the problem. Thanks ...
written 5.4 years ago by mavershang50
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Convert Indel format in vcf
... Hi there, Say I have a insertion (on GRCh37) in format 1    866511    rsXXXXXX    -    CCCT  INFO_Field_BLABLA Is there any existing tools I can use to include the previous ref nucleotide and convert it to 1    866510    rsXXXXXX    A   ACCCT  INFO_Field_BLABLA   Thanks in advance ...
indel snp written 5.4 years ago by mavershang50 • updated 5.4 years ago by Danielk600
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Comment: C: Rename field annotated with SnpSift
... Good idea! I was carried away with snpSift. The only negative side of this solution is that I need to do sed 4 times ...
written 5.4 years ago by mavershang50
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Rename field annotated with SnpSift
... Hi there. I am using "snpSift annotate" to annotate a variant vcf file with two database file also in VCF format (say db1.vcf and db2.vcf). Unfortunately, the fields I am interested in both db VCF files are named "AF", which cause confusion in the output. For example, highlighted 1 990517 ...
snp written 5.4 years ago by mavershang50 • updated 5.4 years ago by Pierre Lindenbaum131k

Latest awards to mavershang

Popular Question 4.3 years ago, created a question with more than 1,000 views. For Rename field annotated with SnpSift
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Variant annotation: Multiple values in some fields like SIFT_Pred
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Calculating coverage for regions with at least 1X for every nucleotide
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Questions running Delly to detect copy number variation
Popular Question 4.3 years ago, created a question with more than 1,000 views. For How to check the reads coverage of an area in ExAC, ESP6500, and 1000Genomes
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Add CADD score to variant annotation using dbNSFP
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Suggestions on miRNA analysis tools/pipeline
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Add CADD score to variant annotation using dbNSFP

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