User: chen

gravatar for chen
chen1.9k
Reputation:
1,870
Status:
Trusted
Location:
OpenGene
Website:
https://github.com/Ope...
Last seen:
5 days, 16 hours ago
Joined:
3 years, 10 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 21 days 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 23 days 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 24 days ago by chen1.9k • updated 22 days ago by Istvan Albert ♦♦ 80k
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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 29 days 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 29 days 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 6 weeks 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 6 weeks 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 6 weeks 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 6 weeks 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 6 weeks ago by chen1.9k

Latest awards to chen

Popular Question 5 weeks ago, created a question with more than 1,000 views. For Why blast result gives Homo sapiens BAC clone
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: How to add read depth to gene of my interest
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Why blast result gives Homo sapiens BAC clone
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How to add read depth to gene of my interest
Appreciated 5 months ago, created a post with more than 5 votes. For A: Good Habit for Bioinformatics Analyst or Scientist
Popular Question 7 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
Popular Question 10 months ago, created a question with more than 1,000 views. For Is there any C API documentation for HTSLIB?
Popular Question 10 months ago, created a question with more than 1,000 views. For Why blast result gives Homo sapiens BAC clone
Popular Question 11 months ago, created a question with more than 1,000 views. For Why blast result gives Homo sapiens BAC clone
Appreciated 11 months ago, created a post with more than 5 votes. For A: Good Habit for Bioinformatics Analyst or Scientist
Popular Question 13 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
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Programming language for Computational Biology
Appreciated 16 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 MutScan: Detect important mutations by scanning FastQ files directly
Scholar 18 months ago, created an answer that has been accepted. For A: How to change the quality score of reads ? (quick help is appreciated)
Appreciated 19 months ago, created a post with more than 5 votes. For MutScan: Detect important mutations by scanning FastQ files directly
Scholar 19 months ago, created an answer that has been accepted. For A: How to change the quality score of reads ? (quick help is appreciated)
Guru 20 months ago, received more than 100 upvotes.
Appreciated 21 months ago, created a post with more than 5 votes. For MutScan: Detect important mutations by scanning FastQ files directly
Appreciated 21 months ago, created a post with more than 5 votes. For MutScan: Detect important mutations by scanning FastQ files directly
Popular Question 21 months ago, created a question with more than 1,000 views. For MutScan: Detect important mutations by scanning FastQ files directly
Centurion 22 months ago, created 100 posts.

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