User: Eric Lim

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Eric Lim1.4k
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Posts by Eric Lim

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Comment: C: Application suggestions for slackbot
... Thanks. Yeah, it's certainly more practical among places which primarily use Slack as the messaging platform. I've always wondered if it will be more applicable toward the general community. ...
written 7 days ago by Eric Lim1.4k
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Forum: Application suggestions for slackbot
... Unsure if this fits here better or the Forum. Over the years, I've developed locally-run Slack bots to perform elementary bioinformatics tasks, i.e. chr1:100-200 to genomic sequence or transcript ID to metadata via Ensembl REST API endpoints. Really simple stuffs but make life a bit easier. If I'm ...
bioinformatics slack forum written 7 days ago by Eric Lim1.4k • updated 7 days ago by RamRS22k
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Comment: C: Mapping exonic sequences across species
... This is one (https://www.ncbi.nlm.nih.gov/pubmed/22369432) and you can download the set at http://tdl.ibms.sinica.edu.tw/OrthoExon/download.html. IIRC, the annotations were hg18 and mm9, so you might need to lift it to newer versions. Earlier this year, I was looking for ways to identify orthologou ...
written 8 days ago by Eric Lim1.4k
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Comment: C: Mapping exonic sequences across species
... Between human and mouse, the published set is generally good enough. As the third-codon position in a coding exon is the least functionally constrained, liftover can fail in capturing some regions in the 2nd species, especially among those that are phylogenetically distant. I've been mostly using li ...
written 9 days ago by Eric Lim1.4k
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Job: Senior Bioinformatics Scientist, Pfenex Inc, San Diego, CA
... Posting for my old boss. Really nice guy. If you're interested, please visit https://pfenex.applicantpro.com/jobs/1083357.html **POSITION SUMMARY** Are you a Bioinformatician, passionate about target identification and validation? Are you keen on working in a multidisciplinary team and experience ...
bioinformatics job written 4 weeks ago by Eric Lim1.4k
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Answer: A: Biopython coding, sublist from list dependently by id
... Not entirely sure the purpose of this grouped list and how Biopython plays a role here. Generally speaking, `groupby` is likely your friend when it comes to stuff like this. from itertools import groupby [[x for x in g] for k,g in groupby(sorted(list_of_ids), lambda x: x.split('/')[0])] ...
written 6 weeks ago by Eric Lim1.4k
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Answer: C: How to mount my data into docker container through -v command?
... Whatever you want. [/scratch/oligo_designer]$ ls references/ GRCh38 [/scratch/oligo_designer]$ docker run -it -v /scratch/oligo_designer/references:/whatever/you/want/ ubuntu:18.04 root@6b3edfb69665:/# ls /whatever/you/want/ GRCh38 root@6b3edfb69665:/# ...
written 6 weeks ago by Eric Lim1.4k
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Comment: C: How to mount my data into docker container through -v command?
... Don't exactly know the difference in PC. There are generally two ways. Assuming the contents of the folder you're adding do not change post-build, you can define something like `ADD . /directory/inside/the/container` in your `Dockerfile` and run `docker` as usual. Alternatively, you can use `docker ...
written 6 weeks ago by Eric Lim1.4k
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Comment: C: What percent of reads should align to a reference gene to successfully validate
... IMHO, this is more of a biological question than a computational one. Whether it's qval, log2fc, or any other relevant measurement, you'll need a predefined set of thresholds to determine a short list of interested genes. Does the differentially expressed gene make biological sense given the experim ...
written 6 weeks ago by Eric Lim1.4k
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Comment: C: Text file: combining lines together based on value within certain column
... I don't think it'd make any difference within the context of what the OP asked. ...
written 6 weeks ago by Eric Lim1.4k

Latest awards to Eric Lim

Scholar 6 weeks ago, created an answer that has been accepted. For A: Two multifasta files with the same sequences, but different headers. How to chan
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For C: How to slice or trim DNA sequence when it encounters NNNN or letters that repres
Teacher 3 months ago, created an answer with at least 3 up-votes. For C: How to slice or trim DNA sequence when it encounters NNNN or letters that repres
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
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: Difference between GTF file with CHR and without CHR. ENSEMBL
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Teacher 11 months ago, created an answer with at least 3 up-votes. For A: How to make your snakefiles self-documenting
Scholar 11 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 11 months ago, created a post with more than 5 votes. For Use a workflow management tool to manage your computational pipelines
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Scholar 12 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 12 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 13 months ago, created an answer with at least 3 up-votes. For A: How to make your snakefiles self-documenting
Scholar 13 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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Scholar 13 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 13 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 18 months ago, created a question with more than 1,000 views. For Use a workflow management tool to manage your computational pipelines
Commentator 21 months ago, created a comment with at least 3 up-votes. For C: Difference between GTF file with CHR and without CHR. ENSEMBL
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