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Search: Posts Made By: chen@haplox.com
Forum: Bioinformatics 12-01-2017, 10:59 PM
Replies: 12
Views: 6,273
Posted By chen@haplox.com
You can use fastp...

You can use fastp (https://github.com/OpenGene/fastp) to preprocess UMI from fastq.
Forum: Bioinformatics 12-01-2017, 10:52 PM
Replies: 2
Views: 1,244
Posted By chen@haplox.com
I suggest fastp...

I suggest fastp (https://github.com/OpenGene/fastp) to do automatic adapter trimming, read filtering and quality control. fastp is ultra-fast since it's developed in C++ and with multi-threading...
Forum: Bioinformatics 12-01-2017, 10:37 PM
Replies: 3
Views: 1,691
Posted By chen@haplox.com
I suggest fastp...

I suggest fastp (https://github.com/OpenGene/fastp) to do automatic adapter trimming, read filtering and quality control. fastp is developed in C++ with multi-threading support, it's ultra-fast.
...
Forum: Bioinformatics 11-08-2017, 10:35 PM
Replies: 0
Views: 1,702
Posted By chen@haplox.com
fastp: a fat all-in-one FASTQ file preprocessor (QC/filter/trim/adapter/split...)

fastp at github: https://github.com/OpenGene/fastp

This tool is designed to provide fast all-in-one preprocessing for FastQ files. It is developed in C++ with multithreading supported to afford...
Forum: Bioinformatics 03-27-2017, 05:27 PM
Replies: 0
Views: 952
Posted By chen@haplox.com
MutScan: detect and visualize mutations by scanning FastQ, 50X faster than pipelines

Introduction

MutScan is a open-source tool to detect target mutations by scanning FastQ files directly. Features:

Ultra sensitive, guarantee that all reads supporting the mutations will be...
Forum: Bioinformatics 05-09-2016, 01:59 AM
Replies: 0
Views: 664
Posted By chen@haplox.com
Are there big DNA level difference of HPV 16/18/31/32 and other HPVs?

I am designing a panel to capture HPV, I wonder if there are big difference of the genomes of HPV 16/18/31/32 and other HPVs? Do I need to design a panel for each one, or just one panel is enough?
Forum: Bioinformatics 05-07-2016, 03:24 PM
Replies: 2
Views: 2,332
Posted By chen@haplox.com
Hi luc, When a sequencer is working, it may...

Hi luc,

When a sequencer is working, it may raise some bubbles from its liquid lanes. Bubbles can affect DNA synthesis reactions and wash processes. According to our investigation, Illumina...
Forum: Bioinformatics 05-07-2016, 05:19 AM
Replies: 2
Views: 2,332
Posted By chen@haplox.com
AfterQC: Automatic Filtering, Trimming, Error Removing and Quality Control for fastq

AfterQC

Code on github: https://github.com/OpenGene/AfterQC

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

AfterQC can simply go through all fastq...
Forum: Bioinformatics 02-19-2016, 06:16 PM
Replies: 2
Views: 1,083
Posted By chen@haplox.com
:D, easy-to-use is required. If you got new...

:D, easy-to-use is required.

If you got new ideas, open an issue to discuss:)
Forum: Bioinformatics 02-19-2016, 05:09 AM
Replies: 2
Views: 1,083
Posted By chen@haplox.com
Introduce OpenGene: an open source genetics library written in Julia

https://github.com/OpenGene/OpenGene.jl

OpenGene, core libraries for NGS data analysis and bioinformatics, written in julia

OpenGene already supports fastq/fasta/vcf/gtf/bed reading and...
Forum: Illumina/Solexa 10-29-2015, 01:08 AM
Replies: 9
Views: 7,319
Posted By chen@haplox.com
And because your read length is extreme short,...

And because your read length is extreme short, you shoud set following parameters:

-p POLY_SIZE_LIMIT, --poly_size_limit=POLY_SIZE_LIMIT
if exists one polyX(polyG means GGGGGGGGG...), and its...
Forum: Illumina/Solexa 10-29-2015, 01:03 AM
Replies: 9
Views: 7,319
Posted By chen@haplox.com
cd to the folder contains your fastq files, and...

cd to the folder contains your fastq files, and try to run with:

python after.py -f0 -t0 -s24

-f0 means no trimming in the front
-t0 means no trimming in the tail
-s24 means set the min read...
Forum: Illumina/Solexa 10-29-2015, 12:28 AM
Replies: 9
Views: 7,319
Posted By chen@haplox.com
What's the error did you meet when using AFTER?...

What's the error did you meet when using AFTER? Let me know that and I will help you to fix it.
Forum: Illumina/Solexa 08-05-2015, 12:15 AM
Replies: 9
Views: 7,319
Posted By chen@haplox.com
Use AFTER to do filtering

AFTER works well with nextseq500 data
Forum: Illumina/Solexa 08-05-2015, 12:07 AM
Replies: 9
Views: 7,319
Posted By chen@haplox.com
Such tool is available on github

There is a tool available on Github for removing PolyA, PolyT, PolyC, PolyG

https://github.com/OpenGene/after

Automatic Filtering, Trimming, and Error Removing for fastq data
Currently it...
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