User: Eric Lim

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Eric Lim1.4k
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Stoke Therapeutics, Inc
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Posts by Eric Lim

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Comment: C: concatenating FASTQ forward and reverse reads in Snakemake
... I generally dislike specifying the entire file path in config, but you can use a function or `lambda` to read those in. These techniques are all clearly described in the documentation, and I'd seriously recommend you spending some time with it. Function as input files: https://snakemake.readthedocs ...
written 24 days ago by Eric Lim1.4k
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Comment: C: concatenating FASTQ forward and reverse reads in Snakemake
... `configfile` will populate what's in the yaml into `config`. As to whether the code will work, there's only one way to find out. ...
written 25 days ago by Eric Lim1.4k
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Answer: A: concatenating FASTQ forward and reverse reads in Snakemake
... What have you tried? Understanding how `wildcards` work can be simple for some and time-consuming for others. I hope this simple example will put you in the right direction. config = { 'samples': { 'a': { 'r1': 'a_r1.txt', 'r2': 'a_r2.txt' } } } rule ...
written 25 days ago by Eric Lim1.4k
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Comment: C: snakemake and Star aligner code issue
... You get the error because `STAR04` doesn't have any wildcard. `{sample}` is already resolved by `expand`, hence `wildcards.sample` is not a valid attribute. Perhaps this post will help. https://www.biostars.org/p/219748/ . Your use of `expand` in both input and output in `STAR04` doesn't make sense ...
written 27 days ago by Eric Lim1.4k
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Answer: A: Biopython Bio.motifs: How to create a motif object with aligned sequences
... The link you referenced above indicates `Bio.motifs.create` takes a list of `Seq` instances. `AlignIO` gives you a list of `SeqRecord` and each of those records has a `Seq` object. So, `[x.seq for x in alignment]` is what you need to provide in `motifs.create`. See below for a working example. ...
written 4 weeks ago by Eric Lim1.4k
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Answer: A: Is there a LIST of available drugs and their target proteins to download?
... You can try https://www.targetvalidation.org, which essentially uses ChEMBL but with nicer interface and API. For example, https://www.targetvalidation.org/evidence/ENSG00000121966/EFO_1000068?view=sec:known_drug I don't know their licensing structure. ...
written 4 weeks ago by Eric Lim1.4k
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Comment: C: Multiz for human-to-mouse and mouse-to-human don't agree with each other
... Thanks Luis. I've asked one of my colleagues to look into this further and will make sure he emails the question to the mailing list. ...
written 10 weeks ago by Eric Lim1.4k
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Comment: C: how to extract unique and the first shared exon in a given gene?
... As @lieven.sterck suggested, `sort -u -k...` should accomplish what you're asking. I don't understand how the following lines are removed, ENSG00000005486 RHBDD2 ENST00000006777 7 75883698 75883848 ENSG00000005486 RHBDD2 ENST00000318622 7 75883698 75883848 and yet ENSG00 ...
written 10 weeks ago by Eric Lim1.4k
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Comment: C: Multiz for human-to-mouse and mouse-to-human don't agree with each other
... Yeah, it's an annotated exon of a gene. I don't really know how to use `compara`, but my random clicking around seems like this region is aligned correctly in Emsembl. ...
written 10 weeks ago by Eric Lim1.4k
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Multiz for human-to-mouse and mouse-to-human don't agree with each other
... I'm not entirely sure what this means and hoping the community can put me in the right direction. In mouse (GRCm38/mm10), the sequence shows decent similarity as human (GRCh38/hg38) with a few mismatches. ![Mouse to human multiz][1] In human (GRCh38/hg38), `=` is used. ![Human to mouse multiz][2 ...
multiz ucsc written 10 weeks ago by Eric Lim1.4k • updated 24 days ago by Biostar ♦♦ 20

Latest awards to Eric Lim

Popular Question 2 days ago, created a question with more than 1,000 views. For Bias, robustness and scalability in single-cell differential expression analysis
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 6 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
Teacher 7 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 8 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 12 months ago, created a comment with at least 3 up-votes. For C: Difference between GTF file with CHR and without CHR. ENSEMBL
Guru 12 months ago, received more than 100 upvotes.
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 15 months ago, created a post with more than 5 votes. For Use a workflow management tool to manage your computational pipelines
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: How to make your snakefiles self-documenting
Centurion 15 months ago, created 100 posts.
Scholar 15 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 16 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 17 months ago, created an answer with at least 3 up-votes. For A: How to make your snakefiles self-documenting
Scholar 17 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 17 months ago, created an answer with at least 3 up-votes. For A: How to make your snakefiles self-documenting
Scholar 17 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 17 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 22 months ago, created a question with more than 1,000 views. For Use a workflow management tool to manage your computational pipelines
Commentator 2.0 years ago, created a comment with at least 3 up-votes. For C: Difference between GTF file with CHR and without CHR. ENSEMBL
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: How to make your snakefiles self-documenting
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