User: chen

gravatar for chen
chen970
Reputation:
970
Status:
Trusted
Location:
Strange Tools: https://github.com/OpenGene
Website:
https://github.com/Ope...
Last seen:
7 hours ago
Joined:
2 years, 1 month ago
Email:
c***@haplox.com

Libraries and tools for NGS data analysis and bioinformatics:

https://github.com/OpenGene

Posts by chen

<prev • 118 results • page 1 of 12 • next >
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Answer: A: Good pratice for clinical NGS data pipelines
... Let me show u an example: https://github.com/OpenGene/ctdna-pipeline A simplified pipeline for ctDNA sequencing data analysis ...
written 1 day ago by chen970
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Answer: A: how to get exact break point in COSMIC fusion gene?
... COSMIC doesn't give the exact break point. But it you want to detect gene fusion with break point, you can try GeneFuse ( https://github.com/OpenGene/GeneFuse ), this tool gives you the break point and the inferred protein. It reports in HTML format and shows interactive information. See an ...
written 8 days ago by chen970
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Answer: A: If it's possible for R detecting the reverse compliment sequence?
... It's quite simple to implement it. I have implemented it in Python, which can be migrated to R without big effort. COMP = {"A" : "T", "T" : "A", "C" : "G", "G" : "C", "a" : "t", "t" : "a", "c" : "g", "g" : "c", "N":"N", "\n":"\n"} def reverse_complement(origin): length = len(or ...
written 8 days ago by chen970
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Answer: A: What is the best way to store clinical and genomic data
... I store the data in a distributed HDFS system. ...
written 15 days ago by chen970
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Comment: C: Any tool to output unmapped or mapped_with_clips reads from a BAM to two fastq f
... But this only output the single reads, not the pair. For pair-end data, if any read of a pair is unmapped or mapped with clips, I'd like to output both reads of this pair. ...
written 18 days ago by chen970
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Any tool to output unmapped or mapped_with_clips reads from a BAM to two fastq files for PE data?
... Hi, I am processing pair-end sequencing data. I want to output the reads that are unmapped to reference genome or mapped with soft/hard clips, to two fastq files (say R1.fq, R2.fq). Is there any existing tool available to do this? If not, I will have to develop it by myself. ...
unmapped bam fastq written 18 days ago by chen970 • updated 18 days ago by Pierre Lindenbaum98k
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Answer: A: Open source projects in next generation sequencing
... Hi KVC, I'm glad that you want to contribute. You can take a look at OpenGene projects (https://github.com/OpenGene ): - [GeneFuse][1]: Gene fusion detection and visualization - [MutScan][2]: Detect and visualize target mutations by scanning FastQ files directly - [OpenGene.jl][3]: OpenGene, co ...
written 18 days ago by chen970 • updated 16 days ago by genomax33k
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Tool: GeneFuse: gene fusion detection and visualization with interactive HTML report
... GeneFuse is a tool to detect and visualize gene fusions. It is written in C++ and only depends on libz library. It can generate interactive HTML report with following information: - the fusion genes, along with their transcripts. - the inferred break point with reference genome coordinations. ...
opengene fusion tool genefuse written 21 days ago by chen970
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Answer: A: Trim Primers from FASTQ file
... If your data is Illumina pair-end sequenced, you can use AfterQC (https://github.com/OpenGene/AfterQC) to trim adapters, without requirement to input the adapter sequences. ...
written 22 days ago by chen970
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Answer: A: Demultiplexing bcl files into fastq files
... I am running bcl2fastq on ubuntu 14.04 and 16.04, both working well. If you cannot run it, post the error messages here. ...
written 28 days ago by chen970

Latest awards to chen

Appreciated 5 days ago, created a post with more than 5 votes. For MutScan: Detect important mutations by scanning FastQ files directly
Appreciated 6 days ago, created a post with more than 5 votes. For MutScan: Detect important mutations by scanning FastQ files directly
Popular Question 16 days ago, created a question with more than 1,000 views. For MutScan: Detect important mutations by scanning FastQ files directly
Centurion 5 weeks ago, created 100 posts.
Good Question 12 weeks ago, asked a question that was upvoted at least 5 times. For How to detect CNV with panel sequencing?
Popular Question 4 months ago, created a question with more than 1,000 views. For MutScan: Detect important mutations by scanning FastQ files directly
Popular Question 5 months ago, created a question with more than 1,000 views. For MutScan: Detect important mutations by scanning FastQ files directly
Appreciated 9 months ago, created a post with more than 5 votes. 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 How to detect CNV with panel sequencing?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Programming language for Computational Biology
Teacher 13 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 16 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 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?
Scholar 17 months ago, created an answer that has been accepted. For A: How to change the quality score of reads ? (quick help is appreciated)
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?
Student 18 months ago, asked a question with at least 3 up-votes. For How to detect CNV with panel sequencing?
Autobiographer 19 months ago, has more than 80 characters in the information field of the user's profile.
Teacher 2.1 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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