User: chen
chen • 970
- Reputation:
- 970
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- Location:
- Strange Tools: https://github.com/OpenGene
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- Last seen:
- 7 hours ago
- Joined:
- 2 years, 1 month ago
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- c***@haplox.com
Libraries and tools for NGS data analysis and bioinformatics:
Posts by chen
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... 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
chen • 970
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... 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
chen • 970
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... 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
chen • 970
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... I store the data in a distributed HDFS system. ...
written 15 days ago by
chen • 970
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... 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
chen • 970
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... 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. ...
written 18 days ago by
chen • 970
• updated
18 days ago by
Pierre Lindenbaum ♦ 98k
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... 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 ...
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... 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. ...
written 21 days ago by
chen • 970
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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
chen • 970
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... 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
chen • 970
Latest awards to chen
Appreciated
5 days ago,
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For MutScan: Detect important mutations by scanning FastQ files directly
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For MutScan: Detect important mutations by scanning FastQ files directly
Popular Question
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For MutScan: Detect important mutations by scanning FastQ files directly
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For How to detect CNV with panel sequencing?
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For MutScan: Detect important mutations by scanning FastQ files directly
Popular Question
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For MutScan: Detect important mutations by scanning FastQ files directly
Appreciated
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For MutScan: Detect important mutations by scanning FastQ files directly
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For How to detect CNV with panel sequencing?
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11 months ago,
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For A: Programming language for Computational Biology
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For AfterQC: Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
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13 months ago,
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For A: Sudden quality drop in the middle of HiSeq R1 reads but not in R2?
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For A: How to change the quality score of reads ? (quick help is appreciated)
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