User: Zhaorong

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Zhaorong1.1k
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State College, PA
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http://azaleasays.com/
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Posts by Zhaorong

<prev • 44 results • page 1 of 5 • next >
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Job: Postdoctoral Positions (Statistical and Population Genetics) in Singapore
... # Posted for a friend. Please see the contact information in the last paragraph.   We are looking for motivated postdoctoral fellows to join a growing research group of statistical and population genetics at the Genome Institute of Singapore (GIS). GIS is a national flagship program for genome scie ...
job genomics population genetics written 2.4 years ago by Zhaorong1.1k
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Comment: C: Where can I download the blast version that includes formatdb ?
... I used the old BLAST on Ubuntu many years ago, so I just found it in Ubuntu packages: http://packages.ubuntu.com/trusty/blast2 I am not sure if it will work on CentOS though. ...
written 2.8 years ago by Zhaorong1.1k
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Answer: A: How to create 10GB blast database
... I may be wrong, but it seems "-max_file_sz" does not allow a size greater than 2GB. Checkout makeblastdb source code line #1122-1126: Uint8 bytes = NStr::StringToUInt8_DataSize(args["max_file_sz"].AsString()); if (bytes >= (1L << 31)) { NCBI_THROW(CInvalidDataException, eInvalidInp ...
written 2.9 years ago by Zhaorong1.1k
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Comment: C: compiliing fasta 3.5 in centos 5.10
... The error message basically says it cannot find the file 'comp_lib2.c'. Make sure that the file exists in the directory of the Makefile. ...
written 3.0 years ago by Zhaorong1.1k
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Comment: C: Process tabular BLAST output
... I would go with a similar workflow, except that I would not store the result in a dictionary if the blast file is huge. Just output the key and value when a new key is encountered. ...
written 3.1 years ago by Zhaorong1.1k
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Comment: C: Problem installing velvet on ubunu 10.04
... See this. Looks like your system is 32-bit? Velvet works only on 64-bit system. See README.txt. ...
written 3.1 years ago by Zhaorong1.1k
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Comment: C: Problem installing velvet on ubunu 10.04
... Try  sudo apt-get install lib64z1-dev ...
written 3.1 years ago by Zhaorong1.1k
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Comment: C: Translate/convert organism prefix in genes names - eg At_geneA, Dd_geneA etc - t
... Two letter prefix are sometimes ambiguous (e.g. Tribolium castaneum (red flour beetle) and Theobroma cacao (cacao)). So my guess is that the prefixes you need to deal with are likely to be commonly seen organisms. So you may want to take a look at the NCBI Taxonomy Browser.  ...
written 3.1 years ago by Zhaorong1.1k
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Answer: A: Problem installing velvet on ubunu 10.04
... It complained about "/usr/bin/ld: cannot find -lz". Looks like this may be of help. Briefly, try sudo apt-get install libz-dev or  sudo apt-get install lib32z1-dev ...
written 3.1 years ago by Zhaorong1.1k
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Comment: C: Annotate Illumina SNP file with Human GRCh37 genes file
... Check the first column of each file and you'll see. :) The "top_level" file has coordinates on assembled chromosomes, i.e. NC_*, while the "scaffolds" file has coordinates on scaffolds (or contigs), e.g. NT_* and NW_*.  ...
written 3.1 years ago by Zhaorong1.1k

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Popular Question 19 months ago, created a question with more than 1,000 views. For How To Set Shrimp Parameters For Best Sensitivity With 35Bp Colorspace Data?
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