User: Eric Lim

gravatar for Eric Lim
Eric Lim870
Reputation:
870
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Boston
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a minute ago
Joined:
2 years, 8 months ago
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k*********@gmail.com

Posts by Eric Lim

<prev • 117 results • page 1 of 12 • next >
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Comment: C: How many reads should I expect for paired end reads when coverage = 30 million?
... It's most likely 15M per end, which is on the low end. As reads can be of varying lengths, I prefer to measure and be quoted by `G` of bases. ...
written 11 hours ago by Eric Lim870
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Comment: C: is Amazon Web Services (AWS) useful?
... I suppose you're interested in `t2.micro` because it's within the Free Tier. Unfortunately, the answer is no. Is AWS (or cloud computing in general) useful? Absolutely. If you've decided on AWS as a provider, I think the following article on `AWS Batch` might be helpful: https://aws.amazon.com/blo ...
written 5 days ago by Eric Lim870
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Comment: C: Error with biopython pairwise aligner
... try `Bio.pairwise2`. http://biopython.org/DIST/docs/api/Bio.pairwise2-module.html ...
written 19 days ago by Eric Lim870
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Answer: A: Command to count reads in fastq file with last bases
... I like the `seqtk` version. You can also use a combination of native commands like `sed`, `rev`, and `cut` to accomplish the same thing and it's easier on the eyes. sed -n '2~4p' input.fq | rev | cut -c1 | sort | uniq -c `sort | uniq -c` is decent for low millions of lines. If your file is lar ...
written 21 days ago by Eric Lim870
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Comment: C: Disease specific mutation database (non cancer)
... https://www.targetvalidation.org/ might be a good starting point. ...
written 21 days ago by Eric Lim870
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Comment: C: Finding polyA site from Ensembl GFF file
... Glad it helps. We implemented a simple motif finding version internally and would be great to hear about your feedback on these tools. ...
written 26 days ago by Eric Lim870
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Comment: C: RNA-seq- Alternative spliceforms
... The gff you posted has `mRNA` entry and that's probably what you're looking for. ...
written 26 days ago by Eric Lim870
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Answer: A: Finding polyA site from Ensembl GFF file
... I'm not aware of any existing tool to find polyA signals directly from GTF. Typically, you need to convert your region coordinates into sequences first. Converting coordinates annotated as 3UTR in your GTF to sequences is a good start. People have implemented various machine learning algorithms, fr ...
written 26 days ago by Eric Lim870
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Answer: A: <3000$ in funding for computer equipment. Should I save this for cloud computing
... Just want to provide some data points for what we pay AWS. Stoke is a small biotech and our entire compute infrastructure is cloud-centric. Our workflow is mostly `snakemake` in `AWS Batch` using spot instances. The figure consists of various genomic experiments we processed in May, totaled over 300 ...
written 4 weeks ago by Eric Lim870
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Comment: C: Quick Way to Annotate a Bed File
... How does `bedtools intersect` not do what you want? Perhaps it's `Chr1` vs `chr1`? ...
written 4 weeks ago by Eric Lim870

Latest awards to Eric Lim

Teacher 21 days ago, created an answer with at least 3 up-votes. For A: How to make your snakefiles self-documenting
Scholar 21 days 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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Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: How to make your snakefiles self-documenting
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Scholar 8 weeks ago, created an answer that has been accepted. For A: Two multifasta files with the same sequences, but different headers. How to chan
Scholar 10 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 3 months ago, created an answer with at least 3 up-votes. For A: How to make your snakefiles self-documenting
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 A: How to make your snakefiles self-documenting
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
Commentator 3 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 8 months ago, created a question with more than 1,000 views. For Use a workflow management tool to manage your computational pipelines
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: Difference between GTF file with CHR and without CHR. ENSEMBL
Teacher 20 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 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
Appreciated 21 months ago, created a post with more than 5 votes. For Use a workflow management tool to manage your computational pipelines
Scholar 22 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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