User: jimmy_zeng

gravatar for jimmy_zeng
jimmy_zeng90
Reputation:
90
Status:
Trusted
Location:
University of Macau
Website:
http://www.bio-info-tr...
Twitter:
jianming_zeng
Last seen:
1 week, 4 days ago
Joined:
3 years, 9 months ago
Email:
u******@gmail.com

A trainee for bioinformatics.

Posts by jimmy_zeng

<prev • 50 results • page 1 of 5 • next >
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Comment: C: RNAseq data anti-pd1 treatment
... Great dataset. Is there any way to download the expression matrix(counts) for PRJEB23709 directly, or we have to download the raw SRA data to process them by using LINUX ? ...
written 27 days ago by jimmy_zeng90
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Comment: C: Pathways Enrichment Analysis.
... why do you update the package at such higher frequency ...
written 12 months ago by jimmy_zeng90
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Answer: A: Issue converting VCF to MAF using snpEff annotations
... I don't think this tool can hold on the vcf files from snpEFF, as below: ``` perl vcf2maf.pl --help Usage: perl vcf2maf.pl --help perl vcf2maf.pl --input-vcf WD4086.vcf --output-maf WD4086.maf --tumor-id WD4086 --normal-id NB4086 Options: --input-vcf Path to input file in VCF ...
written 15 months ago by jimmy_zeng90
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Answer: A: Single Cell RNA-seq Mitochondrial Gene Expression
... I also met that issue, and maybe worse. The gene located in mitochondrial show extremely high reads. ...
written 16 months ago by jimmy_zeng90
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Answer: A: how to analysis HumanOmni5 Exome-4v1-2 Array data ?
... Firstly I used R package "illuminaio" to process the IDAT files to change them to a human readable text format! just like : http://www.biotrainee.com/thread-906-1-1.html and the donwload the mainfest files from Ilumina. but I don't know how to get the AA,BB,AB genotype calls from Mean,NBeads,SD ...
written 2.4 years ago by jimmy_zeng90
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Comment: A: 3-year PhD scholarship available in France
... I will share it to my friends. ...
written 3.0 years ago by jimmy_zeng90
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Comment: C: criteria for choosing proper parameters for MASC2 -- chip-seq ?
... That's exactly what confuse me . Some guys in ENCODE project suggest me to only filter out reads with mapping quality lower than 30. While others suggest that more than 5 or 10 should be keep . maybe it doest matter, I will have a try for both ...
written 3.0 years ago by jimmy_zeng90
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Comment: C: criteria for choosing proper parameters for MASC2 -- chip-seq ?
... I've use the command : **samtools view -bhS -q 30 ${id%%.*}.sam > ${id%%.*}.bam** in my code but I don't know why I should use it ? ...
written 3.0 years ago by jimmy_zeng90
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does peak in CHIP-seq mean the sequence depth in treatment sample will be bigger than control ?
... For a region: sequence depths in control ~~sample is like: **1,2,3,4,4,4,4,4,4,4,4,4,,4,4,4,,4,4,,4,4,4,3,3,2,1** sequence depths in treatment sample is like: **1,2,3,4,5,6,7,8,9,7,7,7,7,7,8,9,8,7,6,5,4,3,2,1,1** so this is the peak , yes or no ?? the depths in treatment must be higher than ...
macs peaks chip-seq written 3.0 years ago by jimmy_zeng90 • updated 3.0 years ago by SP250
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Answer: A: Problem with MACS2 Install?
... ## Download and install macs2 ## // https://pypi.python.org/pypi/MACS2/ cd ~/biosoft mkdir macs2 && cd macs2 wget ~~~~~~~~~~~~~~~~~~~~~~MACS2-2.1.1.20160309.tar.gz tar zxvf MACS2-2.1.1.20160309.tar.gz cd MACS2-2.1.1.20160309 python setup.py install --user Then ...
written 3.0 years ago by jimmy_zeng90

Latest awards to jimmy_zeng

Popular Question 14 months ago, created a question with more than 1,000 views. For criteria for choosing proper parameters for MASC2 -- chip-seq ?
Popular Question 2.4 years ago, created a question with more than 1,000 views. For criteria for choosing proper parameters for MASC2 -- chip-seq ?
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Question: Getgeo Error - line 1 did not have 6 elements
Voter 3.0 years ago, voted more than 100 times.
Supporter 3.2 years ago, voted at least 25 times.
Teacher 3.8 years ago, created an answer with at least 3 up-votes. For A: PhD position in Bioinformatics, Dept. of Bio-New Drug Development, Chosun Univer

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