User: rtliu
rtliu • 2.1k
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Posts by rtliu
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1
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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 ...
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... "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 ...
written 4.7 years ago by
rtliu • 2.1k
• updated
2.1 years ago by
f.hashemigorji • 0
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... 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 4.7 years ago by
rtliu • 2.1k
4
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0
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1.8k
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... 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 ...
written 4.7 years ago by
rtliu • 2.1k
1
vote
1
answer
1.9k
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... 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 4.7 years ago by
rtliu • 2.1k
2
votes
4
answers
6.7k
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4
answers
... 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 4.7 years ago by
rtliu • 2.1k
1
vote
0
answers
2.1k
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0
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... 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 4.7 years ago by
rtliu • 2.1k
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0
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... 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 ...
written 4.8 years ago by
rtliu • 2.1k
6
votes
0
answers
979
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... 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
...
written 4.9 years ago by
rtliu • 2.1k
2
votes
3
answers
6.9k
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3
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... 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 ...
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