User: rtliu

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Posts by rtliu

<prev • 101 results • page 1 of 11 • next >
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Answer: A: Trinity assembly result check
... Supposed you have done proper QC of fastq files (e.g. removing sequencing adaptors),  try normalize reads and assemble the transcript with normalized reads (default 50x coverage):  Trinity --normalize_reads --seqType fq ... Trinity Insilico Normalization   ...
written 2.9 years ago by rtliu2.0k
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News: NCBI NOW (Next generation sequencing Online Workshop) October 13 - 23 , 2015
... "From October 13th to October 23rd, NCBI will present the first iteration of NCBI NOW, a free online experience aimed at those new to next generation sequencing (NGS) analysis. Enrollment in this course is limited to the first 1,000 participants who sign up through the ORAU Portal. Since enrollment ...
ncbi news mapping ngs rna-seq dna-seq written 3.1 years ago by rtliu2.0k • updated 6 months ago by f.hashemigorji0
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Answer: A: Assemble a segment of genome denovo
... You may try Cortex, reference Cortex paper Cortex is an efficient and low-memory software framework for analysis of genomes using sequence data. Cortex allows de novo assembly of variants without having to do a consensus assembly first. Also allows comparison of genomes without using consensus, and ...
written 3.1 years ago by rtliu2.0k
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News: Python for Scientists - FREE Ebook from O'Reilly
... Python for Scientists - A Curated Collection of Chapters from the O'Reilly Data and Programming Libraries Description More and more, scientists are seeing tech seep into their work. From data collection to team management, various tools exist to make your lives easier. But, where to start? Python ...
python news data analysis written 3.1 years ago by rtliu2.0k
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Answer: A: How to set parameters for SOAPdenovo-Trans
... The above fastq data is paired-end, use SRA toolkit to get two fastq files SRR349653_1.fastq and SRR349653_2.fastq . e.g. fastq-dump --split-3 SRR349653 Then set parameters for SOAPdenovo-Trans #fastq file for read 1 q1=/path-to/SRR349653_1.fastq #fastq file for read 2 always follows fastq file ...
written 3.1 years ago by rtliu2.0k
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Comment: C: Install HGAP for de novo PacBio Assembly
... You can run SMRT Portal on the Amazon Cloud using a public machine image that Pacific Biosciences maintains and upgrades - you pay only for the machine time that you use.  - link ...
written 3.2 years ago by rtliu2.0k
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Comment: C: Error with SRA downloaded reads and SPAdes 3.1.0
... Try to download fastq files from ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA068/SRA068445/SRX247326/ Also use full path to fastq files, e.g. spades.py -1 /FULL_PATH_TO_DATASET/SRR769347_1.fastq -2 /FULL_PATH_TO_DATASET/SRR769347_2.fastq ... ...
written 3.2 years ago by rtliu2.0k
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News: Coursera Bioinformatics Specialization will start in August 31 2015
... Coursera Bioinformatics Specialization :  6 courses plus 1 Capstone Description: How do we sequence and compare genomes? How do we identify the genetic basis for disease? We will learn how algorithms and popular software tools are used to answer these and many other questions in modern biology as ...
news coursera written 3.2 years ago by rtliu2.0k
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News: BOSC 2015 slides and videos
... The first BOSC 2015 keynote and all first session "Data Science" videos are posted online, more will follow...... http://www.open-bio.org/wiki/BOSC_2015_Schedule or via youtube Posters and slides: http://f1000research.com/channels/BOSC         ...
bosc2015 news bosc written 3.3 years ago by rtliu2.0k
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Answer: A: cannot import pysam. Module has no attribute error
... It seems your pysam version 0.6 is not up-to-date, try [the latest version](https://pypi.python.org/pypi/pysam): pip install pysam ...
written 3.3 years ago by rtliu2.0k • updated 9 weeks ago by RamRS19k

Latest awards to rtliu

Scholar 2.8 years ago, created an answer that has been accepted. For A: Questions about MaSuRCA assembly program
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: What are the important information should we know about RNA-seq data file before
Scholar 2.9 years ago, created an answer that has been accepted. For A: Questions about MaSuRCA assembly program
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Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: What are the important information should we know about RNA-seq data file before
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Scholar 3.8 years ago, created an answer that has been accepted. For A: Questions about MaSuRCA assembly program
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Good Answer 3.9 years ago, created an answer that was upvoted at least 5 times. For A: What are the important information should we know about RNA-seq data file before

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