User: chen

gravatar for chen
chen1.1k
Reputation:
1,070
Status:
Trusted
Location:
github.com/OpenGene
Website:
https://github.com/Ope...
Last seen:
3 hours ago
Joined:
2 years, 3 months ago
Email:
c***@haplox.com

Libraries and tools for NGS data analysis and bioinformatics:

https://github.com/OpenGene

Posts by chen

<prev • 143 results • page 1 of 15 • next >
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Answer: A: How to extract reads with a known variant form a bam file
... You can try [MutScan](https://github.com/OpenGene/MutScan), input the original FASTQ file and a VCF file that contains your variants. ...
written 1 day ago by chen1.1k
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Answer: A: My run over-clustered - what does this mean for the data?
... The passing filter seems a bit lower than usual, but the data must be still usable. Check the data quality with some QC/filtering tools, like FASTQC or [fastp](https://github.com/OpenGene/fastp) ...
written 1 day ago by chen1.1k
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Answer: A: Illumina Adapter in R1 Only
... In normal case, if R1 has adapters, R2 should also have adapters. But there is an exception: the quality of R2 is much worse than R1 so have too many sequencing errors in the tails of R2. Then, due to the sequencing errors are relative random, the over representation will be reduced. I suggest ...
written 1 day ago by chen1.1k
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Comment: C: Remove hundreds of probes
... I am glad that it helps:) ...
written 1 day ago by chen1.1k
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Answer: A: Remaining adapters ?
... Where are the plenty "AGATCGGAAGAGC" in the read position? Are they in the read tails? Please be noted that normal sequences can also have lots of AGATCGGAAGAGC, since this is too short to be unique for adapters. But if you found they are all near the read tails, that might be adapters, and y ...
written 2 days ago by chen1.1k
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Comment: C: Remove hundreds of probes
... How did you know a half of probes were removed and rest were kept? Can you post the table of adapter trimming result? ...
written 3 days ago by chen1.1k
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Comment: C: NGS on cancer tumor
... You're right, I agree. ...
written 4 days ago by chen1.1k
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Comment: C: NGS on cancer tumor
... You said all mutations are 20% or higher, that's uncommon for a 30% purity tumor. ...
written 4 days ago by chen1.1k
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Comment: A: NGS on cancer tumor
... Was the whole sample used for DNA extraction? Be noted that although the tumor was reported with 30% purity, maybe only a part of the sample with much higher purity was used for DNA extraction. ...
written 4 days ago by chen1.1k
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Comment: C: error while using cutadapt
... I didn't try it since I don't have such data. Would you please send me a sample of nanopore data so that I can fit this tool for nanopore sequence? My email: chen@haplox.com ...
written 6 days ago by chen1.1k

Latest awards to chen

Scholar 2 days ago, created an answer that has been accepted. For A: How to change the quality score of reads ? (quick help is appreciated)
Guru 17 days ago, received more than 100 upvotes.
Appreciated 8 weeks ago, created a post with more than 5 votes. For MutScan: Detect important mutations by scanning FastQ files directly
Appreciated 8 weeks ago, created a post with more than 5 votes. For MutScan: Detect important mutations by scanning FastQ files directly
Popular Question 10 weeks ago, created a question with more than 1,000 views. For MutScan: Detect important mutations by scanning FastQ files directly
Centurion 3 months ago, created 100 posts.
Good Question 4 months ago, asked a question that was upvoted at least 5 times. For How to detect CNV with panel sequencing?
Popular Question 6 months ago, created a question with more than 1,000 views. For MutScan: Detect important mutations by scanning FastQ files directly
Popular Question 6 months ago, created a question with more than 1,000 views. For MutScan: Detect important mutations by scanning FastQ files directly
Appreciated 11 months ago, created a post with more than 5 votes. For MutScan: Detect important mutations by scanning FastQ files directly
Popular Question 11 months ago, created a question with more than 1,000 views. For How to detect CNV with panel sequencing?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Programming language for Computational Biology
Teacher 15 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 18 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 18 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 19 months ago, created an answer that has been accepted. For A: How to change the quality score of reads ? (quick help is appreciated)
Teacher 19 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 20 months ago, asked a question with at least 3 up-votes. For How to detect CNV with panel sequencing?
Autobiographer 21 months ago, has more than 80 characters in the information field of the user's profile.
Teacher 2.3 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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