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:
2 months ago
Joined:
3 years, 5 months ago
Email:
u******@gmail.com

A trainee for bioinformatics.

Posts by jimmy_zeng

<prev • 49 results • page 1 of 5 • next >
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Comment: C: Pathways Enrichment Analysis.
... why do you update the package at such higher frequency ...
written 7 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 10 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 11 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 2.0 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 2.6 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 2.6 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 2.6 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 2.6 years ago by jimmy_zeng90 • updated 2.6 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 2.6 years ago by jimmy_zeng90
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Comment: C: criteria for choosing proper parameters for MASC2 -- chip-seq ?
... yeh, I didn't choose HOMER, just becaues it's a little complicate to install it, I will try it as soon as possible. We have the same problem about how to deal with the alignment files , yes or right ? fiter the bad quality? remove PCR duplicated reads ? ...
written 2.6 years ago by jimmy_zeng90

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Popular Question 10 months ago, created a question with more than 1,000 views. For criteria for choosing proper parameters for MASC2 -- chip-seq ?
Popular Question 24 months ago, created a question with more than 1,000 views. For criteria for choosing proper parameters for MASC2 -- chip-seq ?
Popular Question 24 months ago, created a question with more than 1,000 views. For Question: Getgeo Error - line 1 did not have 6 elements
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Teacher 3.4 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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