User: Eric Lim

gravatar for Eric Lim
Eric Lim560
Reputation:
560
Status:
Trusted
Location:
Stoke Therapeutics, Inc
Website:
http://www.stoketherap...
Twitter:
khericlim
Last seen:
18 minutes ago
Joined:
2 years, 6 months ago
Email:
k*********@gmail.com

Posts by Eric Lim

<prev • 77 results • page 1 of 8 • next >
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Comment: C: Splice junction sites and number of splitted reads from STAR aligned bam
... Too many. While it's old, this should get you started. Good luck! https://www.biostars.org/p/68966/ ...
written 20 hours ago by Eric Lim560
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Best way to systematically select ENCODE data to download?
... I normally use the following link to download ENCODE data. `https://www.encodeproject.org/files/{acc}/@@download/{acc}.fastq.gz` Using the online data selector is certainly one way to figure out the `{acc}`, but I'm wondering if I'm missing an easier way to batch download wanted data from ENCODE. ...
encode written 22 hours ago by Eric Lim560
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Comment: C: Error with snakemake
... Those *.gz files in the repo are not properly compressed. [/scratch/tmp]$ pigz -d sample1_R1.fastq.gz pigz: skipping: sample1_R1.fastq.gz is not compressed pigz: abort: read error on sample1_R1.fastq.gz (Bad file descriptor) [/scratch/tmp]$ mv sample1_R1.fastq.gz sample1_R1.fastq ...
written 4 days ago by Eric Lim560
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Comment: C: samtools and docker
... Instead of using `... biocontainers/samtools index ...`, try `... biocontainers/samtools samtools index ...` and it should work. ...
written 25 days ago by Eric Lim560
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Answer: A: samtools and docker
... Your volume is mounted to `/data`, so you'd need to change your command line to reflect that. docker run -v /home/yey/mdl3/results:/data --rm biocontainers/samtools sort \ -T /tmp/HD753_IonXpress_007.sorted \ -o /data/HD753_IonXpress_007.sorted.bam /data/HD753_IonXpress_007.bam ...
written 25 days ago by Eric Lim560
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Comment: C: Workflows! Where is the code?
... > Do workflows just string together existing tools that other people have created? In the nutshell, yes, but often enough, custom scripts are required to maintain the fluency. Workflow management systems, on the other hand, should provide significantly more functionalities than just stringing ex ...
written 4 weeks ago by Eric Lim560
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Comment: C: How to fillna() in Pandas pivoted tables
... > If you know what will be missing before pivoting the dataframe why not fullfill the dataframe with your new data then pivot ? That's what I ended up doing, which I think it was rather unnecessary. I thought that had to be a simple way to fill values post pivoting. Thank you for your help. ...
written 4 weeks ago by Eric Lim560
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Comment: C: How to fillna() in Pandas pivoted tables
... Perhaps it's better to use the contrived example below: data = [{'gene': 'gene1', 'sj_coord': 'chr1:1-2', 'as_event': 'exon_skipping', 'rep': 'A', 'age': 'E14', 'psj': 1, 'gene_expr': 10}, {'gene': 'gene1', 'sj_coord': 'chr1:10-20', 'as_event': 'exon_inclusion', 'rep': 'A', 'age': ' ...
written 4 weeks ago by Eric Lim560
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How to fillna() in Pandas pivoted tables
... I don't spend much time using pandas. I spent a couple hours yesterday searching on Google but couldn't get it done. While I came up with a hacky workaround, I thought I'd ask the experts here for the pandas' way. The following is a contrived example but should show what I want to accomplish. ...
pandas written 4 weeks ago by Eric Lim560
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Answer: A: changing the name of files
... There are countless ways to accomplish such bash operation, but I always prefer to write simple rules in `snakemake`. # mvfq.py rule: input: expand('{samples}_{reads}.fq.gz', samples=['ALT_1', 'ALT_2'], reads=['R1', 'R2']) rule move_fqs: output: mvto = '{sample}_{read} ...
written 5 weeks ago by Eric Lim560

Latest awards to Eric Lim

Scholar 14 days 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 weeks ago, created an answer with at least 3 up-votes. For A: How to make your snakefiles self-documenting
Scholar 5 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 5 weeks ago, created an answer with at least 3 up-votes. For A: How to make your snakefiles self-documenting
Scholar 5 weeks ago, created an answer that has been accepted. For A: Two multifasta files with the same sequences, but different headers. How to chan
Commentator 6 weeks ago, created a comment with at least 3 up-votes. For C: Difference between GTF file with CHR and without CHR. ENSEMBL
Popular Question 6 months ago, created a question with more than 1,000 views. For Use a workflow management tool to manage your computational pipelines
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
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: How to make your snakefiles self-documenting
Supporter 18 months ago, voted at least 25 times.
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
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

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