User: Lina F

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Lina F80
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80
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Location:
Boston, MA
Last seen:
2 days, 18 hours ago
Joined:
2 years, 8 months ago
Email:
l**********@gmail.com

Posts by Lina F

<prev • 42 results • page 1 of 5 • next >
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Capturing whole gene sequences from WGS metagenomics sample
... 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 ...
assembly metagenomics contigs binning written 3 days ago by Lina F80 • updated 3 days ago by Sej Modha1.3k
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Statistical approach to identifying outliers in RNAseq data?
... 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, ...
outliers detection rna-seq statistics written 8 weeks ago by Lina F80
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Comment: C: Calling SNPs with samtools: how to specify how many supporting observations are
... Thanks for pointing me towards the DP4 field! ...
written 8 weeks ago by Lina F80
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Calling SNPs with samtools: how to specify how many supporting observations are required?
... 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 ...
variant calling samtools snps freebayes written 8 weeks ago by Lina F80 • updated 8 weeks ago by Brian Bushnell12k
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Comment: C: RNAseq transcript quantification: how to deal with different number of genes in
... Thanks for the insight! ...
written 8 weeks ago by Lina F80
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RNAseq transcript quantification: how to deal with different number of genes in host organism?
... 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 ...
sailfish quantification rna-seq transcripts R written 8 weeks ago by Lina F80 • updated 8 weeks ago by h.mon6.6k
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Comment: C: Best reference database for 16S soil datasets?
... 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 F80
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Comment: C: Best reference database for 16S soil datasets?
... Great, I appreciate the input!! ...
written 12 weeks ago by Lina F80
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Best reference database for 16S soil datasets?
... 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! ...
metagenomics reference 16s soil written 12 weeks ago by Lina F80 • updated 12 weeks ago by Denise - Open Targets3.9k
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Comment: C: How to assess biases in ribosomally depleted RNAseq data?
... 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 F80

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