User: fanli.gcb

gravatar for fanli.gcb
fanli.gcb690
Reputation:
690
Status:
Trusted
Location:
Los Angeles, CA
Last seen:
1 year, 10 months ago
Joined:
3 years, 8 months ago
Email:
f********@gmail.com

Sr. Bioinformatics Scientist @ CHLA

Metagenomics // (sc)RNA-seq // ChIP-seq

I mostly use *nix command line tools (Bash, awk) and R. Strangely and sadly bad with Python.

Posts by fanli.gcb

<prev • 88 results • page 1 of 9 • next >
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Comment: C: ggplot2, point with border
... You want to change `scale_colour_manual` to `scale_fill_manual` ...
written 2.3 years ago by fanli.gcb690
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Comment: C: which one is adapter and which one is index
... trim_galore is a wrapper around trimmomatic that will automatically detect and remove common (including Illumina) adapter sequences: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ ...
written 2.4 years ago by fanli.gcb690
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Comment: C: 16S metagenomics data normalization
... Other methods include *not* rarefying: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003531 ...
written 2.6 years ago by fanli.gcb690
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Comment: C: How to install multiple software versions on the same computer?
... I've been using [conda][1] to manage QIIME versions. Since most/all of what you seem to want are Python, that might be a useful approach. [1]: https://conda.io/docs/ ...
written 2.6 years ago by fanli.gcb690
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Comment: C: Best pratices for variant calling on deep sequencing TruSeq Custom Amplicon data
... Would you consider this to also be the case for exome sequencing? ...
written 2.6 years ago by fanli.gcb690
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Answer: A: Size Variation Of The 16S Gene
... An old question, but recently came up in some of our work using the V1V2 (27F-338R) primer set. There seems to be a lot of length variation in our amplicons: ![enter image description here][1] This paper also reports substantial length variation in the V3V4 amplicon (341F-534R): https://www.ncbi.nl ...
written 2.6 years ago by fanli.gcb690
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Comment: C: Using limma for Differential Expression test
... Have you tried following an example from chapter 17 of the limma [tutorial][1]? That got me through the same situation.. [1]: http://www.bioconductor.org/packages/devel/bioc/vignettes/limma/inst/doc/usersguide.pdf ...
written 2.9 years ago by fanli.gcb690
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Comment: C: Motif finding with HOMER
... Did you also grab the homerResults/ and knownResults/ directories from the output folder? The images linked in the HTML are located in those places... ...
written 3.0 years ago by fanli.gcb690
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Comment: C: Weird MA-plot from array data - help?
... Given that all other comparisons (that don't include the 1D timepoint) produce normal looking MA-plots, I have a hard time understanding why code would be an issue. In any case, something like below. Note that I'm using the `plotMA` function from the `limma` package, nothing home rolled. ## set ...
written 3.0 years ago by fanli.gcb690
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Comment: C: FastTreeMP on multicore system
... Huh, then it appears to be configured correctly. Are you sure it's only using one core throughout? There may be certain portions of the tree building that only use a single core ...
written 3.0 years ago by fanli.gcb690

Latest awards to fanli.gcb

Commentator 2.8 years ago, created a comment with at least 3 up-votes. For C: [UPDATE] Thrown into a Bioinformatics Position
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Good Habit for Analyst or Scientist
Rising Star 3.4 years ago, created 50 posts within first three months of joining.
Student 3.4 years ago, asked a question with at least 3 up-votes. For NGS storage on AWS S3
Commentator 3.4 years ago, created a comment with at least 3 up-votes. For C: [UPDATE] Thrown into a Bioinformatics Position
Autobiographer 3.4 years ago, has more than 80 characters in the information field of the user's profile.
Supporter 3.4 years ago, voted at least 25 times.
Appreciated 3.5 years ago, created a post with more than 5 votes. For A: Good Habit for Analyst or Scientist
Good Answer 3.5 years ago, created an answer that was upvoted at least 5 times. For A: Good Habit for Analyst or Scientist
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: Good Habit for Analyst or Scientist

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