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User: chen

gravatar for chen
chen • 1.8k
Reputation:
1,760
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Location:
OpenGene
Website:
https://github.com/Ope...
Last seen:
19 hours ago
Joined:
3 years, 6 months ago
Email:
c***@haplox.com

Libraries and tools for NGS data analysis and bioinformatics:

https://github.com/OpenGene

Posts by chen

<prev • 204 results • page 1 of 21 • next >
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Comment: C: Reduce number of reads from 100M to 50M in the sample from the existing RNA-Seq
... Yes, but the downsampling is not random. fastp just uses the begining reads. ...
written 6 days ago by chen • 1.8k
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Answer: A: Reduce number of reads from 100M to 50M in the sample from the existing RNA-Seq
... Suggest you to use fastp ( https://github.com/OpenGene/fastp ). fastp -i R1.fq.gz -I R2.fq.gz -o out.R1.fq.gz -O out.R2.fq.gz -A -Q -L -G --reads_to_process=50000000 `-A -Q -L -G` options are used to disable quality trimming and adapter trimming, since fastp performs quality and adapter trimm ...
written 6 days ago by chen • 1.8k
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Tool: VisualMSI: detect and visualize microsatellite instability(MSI) from NGS data
... This is a new OpenGene project: https://github.com/OpenGene/VisualMSI # VisualMSI VisualMSI is a tool to detect and visualize microsatellite status from NGS data, by simulating the PCR behavior. VisualMSI extracts the PCR adapters from the reference genome, and tries to map them to the sequencing ...
opengene visualization detection msi tool written 3 months ago by chen • 1.8k
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Comment: C: Can two mates have different file size?
... Read2 is usually bigger than read1 due to its quality is usually lower than read1, which decreases the compression ration. If you want to check whether the PE files are consistent, you can use a tool called PE check: https://github.com/OpenGene/pecheck ...
written 6 months ago by chen • 1.8k
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Comment: C: repaq: compress Illumina FASTQ to be as small as 1/4 of the gzip format.
... Thanks, I will do the benchmark and post the results. ...
written 6 months ago by chen • 1.8k
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Tool: repaq: compress Illumina FASTQ to be as small as 1/4 of the gzip format.
... `repaq` is an open source tool for FASTQ compression: https://github.com/OpenGene/repaq It repacks Illumina format FASTQ to a smaller binary file (.rfq), which can be further compressed by xz or pxz (.rfq.xz). For NovaSeq data, the .rfq file can be much smaller than .fq.gz, and the compressing ...
compress repaq fastq tool written 6 months ago by chen • 1.8k
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Tool: fastp (the ultra-fast all-in-one FASTQ preprocessing tool) v0.18.0 released, 2X faster, with many new features.
... # fastp An open-source tool designed to provide ultra-fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. fastp github repo: https://github.com/OpenGene/fastp # features 0. comprehensive quality profiling for both ...
qc fastp filtering tool written 7 months ago by chen • 1.8k • updated 7 months ago by lena1graham • 0
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Comment: C: quality trimming with trimmomatic
... Thank you, Emily. Your suggestion is good. ...
written 9 months ago by chen • 1.8k
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Comment: C: gencore: a tool to reduce sequencing noises by generating consensus reads
... gencore supports calling consensus reads with or without UMI. Although UMI is not required, it is strongly recommended. If your FASTQ data has UMI integrated, you can use fastp to shift the UMI to read query names. If your data has no UMI, only mapping position information is used to cluster the ...
written 9 months ago by chen • 1.8k
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Answer: A: quality trimming with trimmomatic
... I suggest you to try another quality profiling and trimming tool [fastp](https://github.com/OpenGene/fastp), which is easier to use and is 3x faster than Trimmomatic. ...
written 9 months ago by chen • 1.8k

Latest awards to chen

Appreciated 27 days ago, created a post with more than 5 votes. For A: Good Habit for Bioinformatics Analyst or Scientist
Popular Question 3 months ago, created a question with more than 1,000 views. For Why blast result gives Homo sapiens BAC clone
Popular Question 5 months ago, created a question with more than 1,000 views. For Why blast result gives Homo sapiens BAC clone
Popular Question 5 months ago, created a question with more than 1,000 views. For Is there any C API documentation for HTSLIB?
Popular Question 5 months ago, created a question with more than 1,000 views. For Why blast result gives Homo sapiens BAC clone
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Appreciated 7 months ago, created a post with more than 5 votes. For A: Good Habit for Bioinformatics Analyst or Scientist
Popular Question 8 months ago, created a question with more than 1,000 views. For Why blast result gives Homo sapiens BAC clone
Popular Question 10 months ago, created a question with more than 1,000 views. For Why blast result gives Homo sapiens BAC clone
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Programming language for Computational Biology
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Popular Question 12 months ago, created a question with more than 1,000 views. For Why blast result gives Homo sapiens BAC clone
Popular Question 14 months ago, created a question with more than 1,000 views. For MutScan: Detect important mutations by scanning FastQ files directly
Scholar 14 months ago, created an answer that has been accepted. For A: How to change the quality score of reads ? (quick help is appreciated)
Appreciated 15 months ago, created a post with more than 5 votes. For MutScan: Detect important mutations by scanning FastQ files directly
Scholar 15 months ago, created an answer that has been accepted. For A: How to change the quality score of reads ? (quick help is appreciated)
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Appreciated 17 months ago, created a post with more than 5 votes. For MutScan: Detect important mutations by scanning FastQ files directly
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