User: Eric Lim

gravatar for Eric Lim
Eric Lim1.6k
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Stoke Therapeutics, Inc
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Posts by Eric Lim

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Comment: C: Bioinformatics Server on AWS
... NCBI has an AWS AMI for Blast. My best advice is to start from https://ncbi.github.io/blast-cloud/, then determine if you and your team have the necessary expertise to help this company. ...
written 11 days ago by Eric Lim1.6k
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Answer: A: Snakemake: Force execution of rules in a specific order - ignoring wildcards
... Use `LDSR = expand(rules.ldsr.output, chr=range(1,23))` in your `partitioned_heritability` rule to resolve wildcard `{chr}` and to ensure the rule can only be started after `ldsr` processes all chromosomes. ...
written 11 days ago by Eric Lim1.6k
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Comment: C: GSK Data Strategy & Design Expert
... Pichai is an awesome colleague to work with! ...
written 22 days ago by Eric Lim1.6k
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Comment: C: Generate list of numbers corresponding to fq reads based on 6-character barcode
... What have you tried? The following example isn't the most efficient way, but will get you the count for each first 6 characters in the file. You can use `awk` or `sed` to output every nth line in your fastq that contains the reads. [~/Data/scratch/tmp/biostar]$ cat test.txt GATCGATCGATCG ...
written 3 months ago by Eric Lim1.6k
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Comment: C: how to index different genomes with snakemake with different parameters?
... Sorry for the late response. I was away this weekend. Snakemake's bracket markup only replaces a variable with its string representation. In other words, it doesn't evaluate code. To accomplish what you're trying to do, I'd use something like a `param`. rule get_genome: output: fa="geno ...
written 3 months ago by Eric Lim1.6k
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Comment: C: LiftOver from b37
... https://www.biostars.org/p/153286/ ...
written 3 months ago by Eric Lim1.6k
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Comment: C: Understanding the annotation tag
... I think the first information indicates the region (`utr3_3` indicates 4th exon in utr3, `up` indicates upstream, `cds_13` indicates 14th exon and the exon is coding). The second information indicates the relative position of the indicated region . `NM_001193172_up_2000_chr7_57415651_f` means chr7:5 ...
written 3 months ago by Eric Lim1.6k
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Answer: C: Identifying codons from rna-seq data (bed/bam file)
... Not sure if there's a tool that would turn bed into codons or amino acids. If you were to do this yourself, `bedtools getfasta` (https://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html) is one of the many ways to turn coordinates into sequences. Unless you're translating in all 6 frame ...
written 3 months ago by Eric Lim1.6k
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Comment: C: Big difference in estimated duplicate reads between forward and reverse of paire
... @ATpoint, @genomax, and @h.mom The data are from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE47966 and the discrepancy in estimated duplicates were found in 6 of the 12 human rnaseq samples. Given all the parameters I've looked at, my best guesstimate is that these 12 samples were sequenc ...
written 3 months ago by Eric Lim1.6k
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Comment: C: Big difference in estimated duplicate reads between forward and reverse of paire
... They're relatively older dataset from HiSeq 2000. While patterned flowcells tend to generate more dupes, I'm not sure what is so special about R2? Added: We looked into other fastq parameters (GC contents, adapters, overrepresented sequences, etc) and post-alignment (mapping, skewness, insert sizes ...
written 3 months ago by Eric Lim1.6k

Latest awards to Eric Lim

Teacher 9 days 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 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
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 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
Popular Question 4 months ago, created a question with more than 1,000 views. For Bias, robustness and scalability in single-cell differential expression analysis
Scholar 9 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 10 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 11 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 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 16 months ago, created a comment with at least 3 up-votes. For C: Difference between GTF file with CHR and without CHR. ENSEMBL
Guru 16 months ago, received more than 100 upvotes.
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: How to make your snakefiles self-documenting
Scholar 19 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 19 months ago, created a post with more than 5 votes. For Use a workflow management tool to manage your computational pipelines
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: How to make your snakefiles self-documenting
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Scholar 20 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 21 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 21 months ago, created an answer with at least 3 up-votes. For A: How to make your snakefiles self-documenting
Scholar 21 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 21 months ago, created an answer with at least 3 up-votes. For A: How to make your snakefiles self-documenting
Scholar 21 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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