User: Eric Lim

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Eric Lim1.1k
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Posts by Eric Lim

<prev • 131 results • page 1 of 14 • next >
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Comment: C: Conda on MacOS
... I think the OP might have been mistaken with `wget -O`. His original post, wget https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh bash Miniconda3-latest-MacOSX-x86_64.sh should have been sufficient to install miniconda. I'm not sure where the curl's error came about. ...
written 10 hours ago by Eric Lim1.1k
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Comment: C: 5', 3' ASS and Intron retention read count using STAR out.tab
... You might be interested in tools like SGSeq: https://bioconductor.org/packages/release/bioc/html/SGSeq.html It reads from the aligned bam. It isn't the fastest tool, but from personal experience, it's pretty sensitive for both annotated and novel events. Note: 3'ss and 5'ss stand for 3' splice sit ...
written 12 hours ago by Eric Lim1.1k
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Comment: C: Can snakemake work with multiple nodes from HPC?
... No. Snakemake won't utilize all the cores in the 10 nodes you requested. I'm still trying to wrap my head around on what you're trying to accomplish. Are you doing installation or environment setup via the test.sh? What exactly are you trying to do here? ...
written 3 days ago by Eric Lim1.1k
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Comment: C: Can snakemake work with multiple nodes from HPC?
... Snakemake will run jobs up to using 160 cores in the single machine where snakemake was invoked. Why do you want to qsub the .sh yourself? How do you deal with dependencies among jobs? ...
written 3 days ago by Eric Lim1.1k
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Comment: C: Can snakemake work with multiple nodes from HPC?
... Setting `--cores/--jobs/-j` to 160 is fine. In order to submit jobs to a HPC cluster, you'll, at the very minimum, provide a submit command using `--cluster/-c`. Read https://snakemake.readthedocs.io/en/stable/executable.html#cluster-execution for more information. ...
written 3 days ago by Eric Lim1.1k
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Comment: C: How/where to obtain a bigwig or bedgraph of unmappable genome regions?
... It's been a long time since I used `gem`. Are you looking for something like this? https://wiki.bits.vib.be/index.php/Create_a_mappability_track ...
written 4 days ago by Eric Lim1.1k
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Answer: A: How to write the output in snakefile (snakemake) for bowtie2-build
... IP's solution is best as expected outputs are listed explicitly which would take advantage of timestamp. Since v5.2.0, you can also accomplish this by using `directory`, which shorten the code by quite a bit while maintaining timestamp, but snakemake won't check if all expected outputs exist. ...
written 7 days ago by Eric Lim1.1k
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Comment: C: CLIP-seq database contains PAR-CLIP, HITS-CLIP, iCLIP, eCLIP, dCLIP, CLASH, CLEA
... Thanks! I noticed there are 2 relatively well cited Rfbox papers were not included? https://www.ncbi.nlm.nih.gov/pubmed/29398366 https://www.ncbi.nlm.nih.gov/pubmed/24613350 ...
written 24 days ago by Eric Lim1.1k
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Answer: A: Which database software is better for bioinformatics web development? MySQL or M
... Micheal has given and asked some really excellent questions, so I'll just share what we've been doing. Our approach is developing and deploying events driven web applications using serverless technology (https://aws.amazon.com/lambda/ ) and couple these applications with various serverless database ...
written 29 days ago by Eric Lim1.1k • updated 29 days ago by genomax57k
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Answer: C: Get gene nams from ensembl ID or gene region
... Their REST is probably the quickest, especially for single ID/gene lookup https://rest.ensembl.org/documentation/info/lookup https://rest.ensembl.org/documentation/ ...
written 5 weeks ago by Eric Lim1.1k

Latest awards to Eric Lim

Guru 3 days ago, received more than 100 upvotes.
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: How to make your snakefiles self-documenting
Scholar 11 weeks ago, created an answer that has been accepted. For A: Two multifasta files with the same sequences, but different headers. How to chan
Appreciated 3 months ago, created a post with more than 5 votes. For Use a workflow management tool to manage your computational pipelines
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How to make your snakefiles self-documenting
Centurion 3 months ago, created 100 posts.
Scholar 3 months ago, created an answer that has been accepted. For A: Two multifasta files with the same sequences, but different headers. How to chan
Scholar 4 months ago, created an answer that has been accepted. For A: Two multifasta files with the same sequences, but different headers. How to chan
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How to make your snakefiles self-documenting
Scholar 5 months ago, created an answer that has been accepted. For A: Two multifasta files with the same sequences, but different headers. How to chan
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How to make your snakefiles self-documenting
Scholar 5 months ago, created an answer that has been accepted. For A: Two multifasta files with the same sequences, but different headers. How to chan
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Difference between GTF file with CHR and without CHR. ENSEMBL
Popular Question 10 months ago, created a question with more than 1,000 views. For Use a workflow management tool to manage your computational pipelines
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: Difference between GTF file with CHR and without CHR. ENSEMBL
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: How to make your snakefiles self-documenting
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Teacher 23 months ago, created an answer with at least 3 up-votes. For A: How to make your snakefiles self-documenting
Scholar 23 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 23 months ago, created a post with more than 5 votes. For Use a workflow management tool to manage your computational pipelines
Scholar 24 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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