User: chen

gravatar for chen
chen1.4k
Reputation:
1,380
Status:
Trusted
Location:
OpenGene
Website:
https://github.com/Ope...
Last seen:
17 hours ago
Joined:
2 years, 5 months ago
Email:
c***@haplox.com

Libraries and tools for NGS data analysis and bioinformatics:

https://github.com/OpenGene

Posts by chen

<prev • 184 results • page 1 of 19 • next >
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Answer: A: Faster reading sequences from a fastq file
... You can try the code of [fastp](https://github.com/OpenGene/fastp), which provides ultra-fast FASTQ file preprocessing. You may look into the [src/fastqreader.cpp](https://github.com/OpenGene/fastp/blob/master/src/fastqreader.cpp) which provides a almost-standalone C++ class to read FASTQ file, and ...
written 2 days ago by chen1.4k
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Tool: fastp, the ultra-fast FASTQ preprocessing tool, is now on BioConda
... [fastp](https://github.com/OpenGene/fastp) is a 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. # Features: 1. filter out bad reads (too low quality, too short, or too many N... ...
tutorial fastp tool written 9 days ago by chen1.4k
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Comment: C: AfterQC: Automatic Filtering, Trimming, Error Removing and Quality Control for f
... AfterQC doesn't support multi-threading since it's in Python, you can use another tool I developed, which is much faster and more powerful -- [fastp](https://github.com/OpenGene/fastp) ...
written 11 days ago by chen1.4k
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Comment: C: SAMTOOLS installation errore
... I think the file you downloaded is the source code of samtools, you need to compile it instead of installing it by dpkg ...
written 13 days ago by chen1.4k
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Comment: C: How to remove the empty line in using python
... `rstrip()` should be better than `strip()` to avoid unwanted trimming in the head of line ...
written 13 days ago by chen1.4k
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Comment: C: How to remove the empty line in using python
... `print()` will automatically add a line break in the tail ...
written 14 days ago by chen1.4k
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Answer: A: How to remove the empty line in using python
... This is my guess: 1, your use readline() to get lines from the original file 2, when you use write() to write lines to the new file, you append a `\n` into the tail of each line I can take a look at your code if you post it ...
written 14 days ago by chen1.4k
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Answer: A: kmer Counter using hadoop and gpu
... GPU will definitely help, you can try `CUDA` from NVIDIA for GPU programming. ...
written 18 days ago by chen1.4k
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Comment: C: quality filtering error usearch
... Could you point out where is this `fastqfilter.cpp`, that will be helpful to locate your problem. BTW, [fastp](https://github.com/OpenGene/fastp) may help you to do the trimming and filtering. fastp is a ultra-fast open-source FASTQ preprocessing tool developed in C++, with following features: ...
written 18 days ago by chen1.4k
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Answer: A: Minimum read length in Trimmomatic
... You can decrease it, but too short read may cause misalignment. And it depends on your data, if you're processing micro RNA, you should decrease it to less than 20, since micro RNA is usually 20~25 bp long. ...
written 25 days ago by chen1.4k

Latest awards to chen

Popular Question 4 weeks ago, created a question with more than 1,000 views. For MutScan: Detect important mutations by scanning FastQ files directly
Scholar 5 weeks ago, created an answer that has been accepted. For A: How to change the quality score of reads ? (quick help is appreciated)
Appreciated 8 weeks ago, created a post with more than 5 votes. For MutScan: Detect important mutations by scanning FastQ files directly
Scholar 9 weeks ago, created an answer that has been accepted. For A: How to change the quality score of reads ? (quick help is appreciated)
Guru 11 weeks ago, received more than 100 upvotes.
Appreciated 4 months ago, created a post with more than 5 votes. For MutScan: Detect important mutations by scanning FastQ files directly
Appreciated 4 months ago, created a post with more than 5 votes. For MutScan: Detect important mutations by scanning FastQ files directly
Popular Question 4 months ago, created a question with more than 1,000 views. For MutScan: Detect important mutations by scanning FastQ files directly
Centurion 5 months ago, created 100 posts.
Good Question 6 months ago, asked a question that was upvoted at least 5 times. For How to detect CNV with panel sequencing?
Popular Question 8 months ago, created a question with more than 1,000 views. For MutScan: Detect important mutations by scanning FastQ files directly
Popular Question 9 months ago, created a question with more than 1,000 views. For MutScan: Detect important mutations by scanning FastQ files directly
Appreciated 13 months ago, created a post with more than 5 votes. For MutScan: Detect important mutations by scanning FastQ files directly
Popular Question 13 months ago, created a question with more than 1,000 views. For How to detect CNV with panel sequencing?
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Programming language for Computational Biology
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Sudden quality drop in the middle of HiSeq R1 reads but not in R2?
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Sudden quality drop in the middle of HiSeq R1 reads but not in R2?
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Sudden quality drop in the middle of HiSeq R1 reads but not in R2?
Scholar 21 months ago, created an answer that has been accepted. For A: How to change the quality score of reads ? (quick help is appreciated)
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Sudden quality drop in the middle of HiSeq R1 reads but not in R2?
Student 22 months ago, asked a question with at least 3 up-votes. For How to detect CNV with panel sequencing?
Autobiographer 23 months ago, has more than 80 characters in the information field of the user's profile.
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Sudden quality drop in the middle of HiSeq R1 reads but not in R2?

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