User: chen

gravatar for chen
chen1.9k
Reputation:
1,930
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Location:
OpenGene
Website:
https://github.com/Ope...
Last seen:
3 months, 1 week ago
Joined:
4 years, 2 months ago
Email:
c***@haplox.com

Libraries and tools for NGS data analysis and bioinformatics:

https://github.com/OpenGene

Posts by chen

<prev • 216 results • page 1 of 22 • next >
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Comment: C: Do you need a deduplication tool for FASTQ data in fastp?
... Thanks for your advice. ...
written 4 months ago by chen1.9k
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Comment: C: Do you need a deduplication tool for FASTQ data in fastp?
... Thanks, I will consider your suggestion. For deduplication, I think I can control the RAM usage to be less than 16G for processing even 1Tbp Illumina PE data. ...
written 4 months ago by chen1.9k
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Forum: Do you need a deduplication tool for FASTQ data in fastp?
... Hi, I am the author of [fastp][1], a tool to provide ultra-fast all-in-one FASTQ preprocessing functions. This tool has received 500+ stars in github (https://github.com/OpenGene/fastp), and has been cited for 40+ times since its [paper][2] published in Bioinformatics about 8 months ago. Now I am ...
forum fastp deduplication written 4 months ago by chen1.9k • updated 4 months ago by Istvan Albert ♦♦ 81k
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Answer: A: Find illumina adaptors
... Normally they are Illumina TruSeq adapters. If you don't know it, use [fastp][1] to detect the adapters automatically. See https://github.com/OpenGene/fastp#adapters for details. Remind to enable `--detect_adapter_for_pe` option if your nextseq 500 data is paired-end. [1]: https://github.com/ ...
written 4 months ago by chen1.9k
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Answer: A: How to blast a paired end fastq file?
... You can use [fastp][1] to merge it first, then blast the merged reads See the intro here: https://github.com/OpenGene/fastp#merge-paired-end-reads [1]: https://github.com/OpenGene/fastp ...
written 4 months ago by chen1.9k
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Comment: C: help in Language
... If you only want one language, then go with Python first. ...
written 5 months ago by chen1.9k
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Comment: C: very confused with GC bias
... Some sequencers, like Illumina NovaSeq may have polyG in end of reads, which may affect GC curve. Use fastp to trim polyG and check the post-filtering data. ...
written 5 months ago by chen1.9k
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Answer: A: help in Language
... For biological background graduates, Python and R should be the best languages to learn. ...
written 5 months ago by chen1.9k
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Answer: A: Generating consensus sequence from bam file
... try gencore: https://github.com/OpenGene/gencore Generate consensus reads to reduce sequencing noises and remove duplications ...
written 5 months ago by chen1.9k
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Comment: C: How to evaluate correlation for multiple measurements per point?
... Yo should be aware of position-related sequencing artifacts ...
written 5 months ago by chen1.9k

Latest awards to chen

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
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How to add read depth to gene of my interest
Popular Question 6 months ago, created a question with more than 1,000 views. For Why blast result gives Homo sapiens BAC clone
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: How to add read depth to gene of my interest
Appreciated 9 months ago, created a post with more than 5 votes. For A: Good Habit for Bioinformatics Analyst or Scientist
Popular Question 11 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 Why blast result gives Homo sapiens BAC clone
Popular Question 14 months ago, created a question with more than 1,000 views. For Is there any C API documentation for HTSLIB?
Popular Question 14 months ago, created a question with more than 1,000 views. For Why blast result gives Homo sapiens BAC clone
Popular Question 15 months ago, created a question with more than 1,000 views. For Why blast result gives Homo sapiens BAC clone
Appreciated 15 months ago, created a post with more than 5 votes. For A: Good Habit for Bioinformatics Analyst or Scientist
Popular Question 17 months ago, created a question with more than 1,000 views. For Why blast result gives Homo sapiens BAC clone
Popular Question 18 months ago, created a question with more than 1,000 views. For Why blast result gives Homo sapiens BAC clone
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Programming language for Computational Biology
Appreciated 20 months ago, created a post with more than 5 votes. For A: Good Habit for Bioinformatics Analyst or Scientist
Popular Question 21 months ago, created a question with more than 1,000 views. For Why blast result gives Homo sapiens BAC clone
Popular Question 22 months ago, created a question with more than 1,000 views. For MutScan: Detect important mutations by scanning FastQ files directly
Scholar 22 months ago, created an answer that has been accepted. For A: How to change the quality score of reads ? (quick help is appreciated)
Appreciated 23 months ago, created a post with more than 5 votes. For MutScan: Detect important mutations by scanning FastQ files directly
Scholar 23 months ago, created an answer that has been accepted. For A: How to change the quality score of reads ? (quick help is appreciated)
Guru 24 months ago, received more than 100 upvotes.
Appreciated 2.1 years ago, created a post with more than 5 votes. For MutScan: Detect important mutations by scanning FastQ files directly
Appreciated 2.1 years ago, created a post with more than 5 votes. For MutScan: Detect important mutations by scanning FastQ files directly
Popular Question 2.1 years ago, created a question with more than 1,000 views. For MutScan: Detect important mutations by scanning FastQ files directly

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