User: Yang Li

gravatar for Yang Li
Yang Li70
Reputation:
70
Status:
Trusted
Location:
China
Last seen:
3 years, 10 months ago
Joined:
4 years, 9 months ago
Email:
y*******@gmail.com

MSc in Biomedical Engineering

Posts by Yang Li

<prev • 10 results • page 1 of 1 • next >
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(Closed) Centos 6.3 (Final) ETE: cannot connect to X server
... Hi, there   I used ETE to visualize the phylogenetic tree. The script worked at ubuntu 14.04 LTS (Desktop) but failed on remote server which ran Centos 6.3.   Here are the commands and returns: python script ** ETE: cannot connect to X server ***I googled some methods and tested them env DIS ...
ete written 3.9 years ago by Yang Li70
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Tool: NGS Data Analysis Pipeline for Virus Identification
... Hi, there   About 5 months ago, I firstly introduced a pipeline for virus identification which was under developing. (https://www.biostars.org/p/120708/#120885) Now core parts for the pipeline have been achieved, We put 2 sets of results of the pipeline online using biological NGS datasets generate ...
tool virus written 4.3 years ago by Yang Li70
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Comment: C: de novo assembly v.s. genome guided assembly (Trinity) -- better N50 from de nov
... Thank you. How to value the quality of assembly? I tried to extract the longest contig from above four strategy and blast them. The results showed no significantly difference from blast results. (Coverage: 100%, Identity: 99%, E-value: down to 0). ...
written 4.5 years ago by Yang Li70
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Comment: C: De novo assembly for virus genome with Velvet.
... Try normalization the reads before assembly. http://ged.msu.edu/papers/2012-diginorm/ ...
written 4.5 years ago by Yang Li70
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Comment: C: de novo assembly v.s. genome guided assembly (Trinity) -- better N50 from de nov
... Thank you. Could you give me some advice to generate a longer contig? Because sequencing strategy used in PGM is single end, tools such as SSPACE were developed for paired-end reads.  ...
written 4.5 years ago by Yang Li70
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de novo assembly v.s. genome guided assembly (Trinity) -- better N50 from de novo than genome guided
... Hi, there       I made a test for virus assembly using Trinity (2.02). The results as followings: 1, normalize before assembly Trinity --normalize_reads --seqType fa --max_memory 5G --single temp.Flavivirus.fa --CPU 6 prinseq-lite.pl -stats_assembly -fasta ./trinity_out_dir/Trinity.fasta stats_as ...
assembly virus assembly rna-seq trinity written 4.5 years ago by Yang Li70 • updated 4.5 years ago by 5heikki8.5k
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Comment: C: Shall we perform a bio-experiment like PCR to confirm bioinformatics analysis?
... Thank you. I will release it on github when it is ready. I will appreciate your comments。 ...
written 4.8 years ago by Yang Li70
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Comment: A: Shall we perform a bio-experiment like PCR to confirm bioinformatics analysis?
... Because of my job I know lots of clinical samples can not be characterized. A story happened to me is an infant suffered diarrhea with unknown reason. Colleagues here finally found out sapovirus infection after 7 days. During the 7 days, doctors used every methods to keep its life with a heavy cost ...
written 4.8 years ago by Yang Li70
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Comment: C: Shall we perform a bio-experiment like PCR to confirm bioinformatics analysis?
... Thank you for suggestions. The program or the pipeline is based on scripts based on Perl/Shell/Python. These scripts are used to combine the open-source tools together. Sets of public data has been used to test the pipeline. As Ryan said "The more skeptical you are of your own results early on, the ...
written 4.8 years ago by Yang Li70
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Shall we perform a bio-experiment like PCR to confirm bioinformatics analysis?
... Hi, With an in-house program developed by myself, the following information from the NGS result can be got: ref_gi species genus %coverage reads_hit Now the result suggests that a virus with coverage more than 90%. Then I assemble the reads guided by the reference, nearly complete genome of this ...
metagenomics next-gen written 4.8 years ago by Yang Li70

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