User: chen
chen • 1.9k
- 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:
Posts by chen
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0
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201
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... Thanks for your advice. ...
written 21 days ago by
chen • 1.9k
0
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2
answers
201
views
2
answers
... 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
chen • 1.9k
4
votes
2
answers
201
views
5 follow
2
answers
... 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 ...
written 24 days ago by
chen • 1.9k
• updated
22 days ago by
Istvan Albert ♦♦ 80k
0
votes
2
answers
149
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2
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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
chen • 1.9k
0
votes
2
answers
186
views
2
answers
... 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
chen • 1.9k
2
votes
2
answers
233
views
2
answers
Comment:
C: help in Language
... If you only want one language, then go with Python first. ...
written 6 weeks ago by
chen • 1.9k
0
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4
answers
298
views
4
answers
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
chen • 1.9k
3
votes
2
answers
233
views
2
answers
Answer:
A: help in Language
... For biological background graduates, Python and R should be the best languages to learn. ...
written 6 weeks ago by
chen • 1.9k
0
votes
5
answers
465
views
5
answers
... try gencore: https://github.com/OpenGene/gencore
Generate consensus reads to reduce sequencing noises and remove duplications ...
written 6 weeks ago by
chen • 1.9k
0
votes
1
answer
125
views
1
answers
... Yo should be aware of position-related sequencing artifacts ...
written 6 weeks ago by
chen • 1.9k
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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