User: Lina F
Lina F • 80
- Reputation:
- 80
- Status:
- Trusted
- Location:
- Boston, MA
- Last seen:
- 2 days, 18 hours ago
- Joined:
- 2 years, 8 months ago
- Email:
- l**********@gmail.com
Posts by Lina F
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... Hi all,
I have a metagenomics dataset and I am interested in retrieving full or nearly complete gene sequences.
I first tried assembling the data using Ray Meta to assemble the data. The average length of my contigs is between 700 and 900 bp long.
How can I further resolve these contigs?
My firs ...
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... Hi All,
I am looking at a larger RNAseq dataset (144 samples) and I did some exploratory data analysis to look at clustering. From the PCA plot, it looks like there is a sample that clusters with a different group than expected (see the blue dot below among all the red dots). Based on this figure, ...
written 8 weeks ago by
Lina F • 80
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... Thanks for pointing me towards the DP4 field! ...
written 8 weeks ago by
Lina F • 80
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... Hi all,
I am interested in calling SNPs for some alignment data that I have. I am looking at solutions with `samtools mpileup` and `freebayes`.
I noticed that freebayes has an option to specify how many observations have to support a variant before it is called (the `-C` option).
Is there somethi ...
written 8 weeks ago by
Lina F • 80
• updated
8 weeks ago by
Brian Bushnell ♦ 12k
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... Thanks for the insight! ...
written 8 weeks ago by
Lina F • 80
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... Hi all,
I have RNAseq datasets from two organisms: one is the basic E. coli organism and the other one is the same E. coli, but I engineered it and added a gene. Now I would like to perform an RNAseq experiment and compare the differentially expressed genes.
I plan on quantifying the transcripts u ...
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... Thanks for the link! However, these look like metagenomics samples, not necessarily reference databases for use in annotation taxonomies, or am I missing something? ...
written 12 weeks ago by
Lina F • 80
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... Great, I appreciate the input!! ...
written 12 weeks ago by
Lina F • 80
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... Hi all,
I came across some interesting 16S datasets from soil. Can anyone recommend a good reference database? RDP vs Silva? The Greengenes webpage highlights the update from May 2013... so maybe a bit outdated.
Thanks for your suggestions! ...
written 12 weeks ago by
Lina F • 80
• updated
12 weeks ago by
Denise - Open Targets • 3.9k
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... Could you elaborate on how to correlate the data?
I plotted three samples below that were treated with three different rRNA depletion protocols. The third protocol removed the most rRNA (i.e. the percentage value on the 2nd y-axis is highest).
![enter image description here][1]
![enter image desc ...
written 3 months ago by
Lina F • 80
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