User: dmj6ab

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dmj6ab10
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Posts by dmj6ab

<prev • 7 results • page 1 of 1 • next >
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Comment: C: Database Recommendations for 16S-seq of the V4 Region
... For my particular dataset (mouse gut microbiome), GTDB did a good job of recapitulating the "keystone" taxa from the original Greengenes-based taxonomy, resulting in similar compositions of *Lactobacillus* and clostridia/bacilli abundance ratios. I'm favoring GTDB at the moment because it's doing ...
written 5 weeks ago by dmj6ab10
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Database Recommendations for 16S-seq of the V4 Region
... Hello, I have been working on a 16S-seq microbiome abundance experiment analysis for quite some time and I still can't decide which database I should use to assign taxonomy. As a background, I recently switched over from QIIME to DADA2 and I am deciding between SILVA, RDP, and the Genome Taxonomy D ...
microbiome taxonomy silva 16s-seq dada2 written 7 weeks ago by dmj6ab10
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Comment: C: Advice on Handling Batch Effect in ChIP-seq Experiment
... Thanks Colin for all the help. I checked with my collaborator recently and they shared the troubleshooting data with me. It seems that the antibody they were using for rev-erba had poor performance (low affinity) and the fragment lengths were anything but uniform (anywhere from 100 bases up to 1kb), ...
written 10 weeks ago by dmj6ab10
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Comment: C: Advice on Handling Batch Effect in CHiP-seq Experiment
... Thanks for the insight. FRiP was one of the next few things that I was going to look at. You're right about PCR duplication, there were an obscenely high (Given that this is TF CHiP-seq) number of reads in each sample (~30 million), so PCR duplication is almost a guarantee to some extent at least. W ...
written 12 weeks ago by dmj6ab10
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Advice on Handling Batch Effect in ChIP-seq Experiment
... I am currently working on a ChIP-seq experiment with a collaborator and I'm running into problems that may be due to the overall experimental design. So for an overall background, I was brought on as a bioinformatics analyst after the experiment was ordered and sequenced. From what I know so far t ...
replicates sequencing chip-seq batch effect batch written 12 weeks ago by dmj6ab10
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Does anyone have experience with setting parameters for thresholding/image analysis with Skan?
... Hello, I am affiliated with a project that is interested in quantifying number and length of axonal tracts in whole-brain images of mice. I came upon Skan (https://jni.github.io/skan/getting_started.html) as a potential tool for this problem. While it was designed for blood vessel analysis, I see p ...
neuroscience python image analysis skan sauvola written 3 months ago by dmj6ab10
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Using FastTree to Constrian by Taxonomy
... I've recently completed a 16S project using a phylogenetic tree with aligned OTUs from QIIME. I got through the analysis without too many issues, but for the purpose of publication, we would like an "unaligned" tree with a topology that represents only the known taxonomy of a given tip (as opposed t ...
alignment 16s taxonomy constraints fasttree written 2.4 years ago by dmj6ab10

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