User: Eric Lim

gravatar for Eric Lim
Eric Lim370
Reputation:
370
Status:
Trusted
Location:
Stoke Therapeutics, Inc
Website:
http://www.stoketherap...
Twitter:
khericlim
Last seen:
3 minutes ago
Joined:
2 years, 1 month ago
Email:
k*********@gmail.com

Posts by Eric Lim

<prev • 49 results • page 1 of 5 • next >
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Comment: C: I'm putting a pipeline into docker, where do I store the tar files for my depend
... Totally up to you. If the file is local, you can use `ADD` or `COPY`. Look up the documentation to determine which one is more applicable to your use case. If it's stored somewhere online accessible without credentials, you can just `wget` or `git clone `and proceed to the installation as usual. ...
written 4 days ago by Eric Lim370
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Answer: A: I'm putting a pipeline into docker, where do I store the tar files for my depend
... I typically use conda. RUN mkdir -p /tmp/conda-build && wget -nv https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh && bash Miniconda3-latest-Linux-x86_64.sh -b -p /miniconda3 RUN cp /miniconda3/bin/conda /miniconda3/bin/conda3 ENV PATH=/miniconda3/bi ...
written 4 days ago by Eric Lim370
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Job: Scientist/Senior Scientist, Bioinformatics at Stoke Therapeutics, Inc, Bedford, MA, USA
... Stoke is seeking to hire a scientist/senior scientist with a strong record of success in bioinformatics. Candidates must hold a Ph.D. degree in bioinformatics, a record of peer-reviewed publications, and at least 0-4 years of post-graduate experience in applied research. Research experience in RNA ...
bioinformatics splicing job rna biology written 26 days ago by Eric Lim370 • updated 26 days ago by genomax40k
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Answer: A: Doing RNA folding online for 1200 nt long sequence
... In addition to RNAfold, Sfold: http://sfold.wadsworth.org/cgi-bin/index.pl Mfold: http://unafold.rna.albany.edu/?q=mfold/RNA-Folding-Form ...
written 28 days ago by Eric Lim370
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Comment: C: Bioinformatic or bioinformatics?
... I always just use computational. Computational engine sounds a heck lot fancier than bioinformatics tools/workflows. ;) ...
written 29 days ago by Eric Lim370
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Comment: C: Sequence Data Management
... While it's not a database, I've had success using HDF5 for various projects. ...
written 4 weeks ago by Eric Lim370
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Comment: C: is always necessary to do an intermediate index generations and 2nd pass alignme
... The 2-pass mode isn't required to detect novel junctions. The 2nd step, however, does increase the mapping of detected novel junctions. Star 2-pass is most commonly used by combining all the sj files from the first pass. You can either use `--sjdbFileChrStartEnd` to provide a list of sj files (on-th ...
written 6 weeks ago by Eric Lim370
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Comment: C: Extracting 5'UTR and 3'UTR bed files from gtf file
... GTFs downloaded from Gencode have UTR annotations. The designation of 3' and 5' can be derived from the UTR coordinates and their corresponding strand. ...
written 9 weeks ago by Eric Lim370
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Answer: A: How to make your snakefiles self-documenting
... Not sure if this is a newly added functionality, but I just realized one can simply do `snakemake -l` or `snakemake --lt` to display docstrings for each rule. This is better than what I've been doing: rule print_help: """Print help menu. """ run: tbl = PrettyTable(['Rules', 'Description'] ...
written 10 months ago by Eric Lim370
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Comment: C: Genome Browser and Custom Tracks
... For the example above, I got all the variants for SF3B1 via the export function from the web application, copied the 3 columns that contain chromosome, position, and allele frequencies, and pasted into Genome Graph. To automate the entire genome, I assume it's very doable by simply transforming the ...
written 11 months ago by Eric Lim370

Latest awards to Eric Lim

Popular Question 5 weeks ago, created a question with more than 1,000 views. For Use a workflow management tool to manage your computational pipelines
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Difference between GTF file with CHR and without CHR. ENSEMBL
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: How to make your snakefiles self-documenting
Supporter 13 months ago, voted at least 25 times.
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: How to make your snakefiles self-documenting
Scholar 14 months ago, created an answer that has been accepted. For A: Two multifasta files with the same sequences, but different headers. How to chan
Appreciated 14 months ago, created a post with more than 5 votes. For Use a workflow management tool to manage your computational pipelines
Scholar 14 months ago, created an answer that has been accepted. For A: Two multifasta files with the same sequences, but different headers. How to chan

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