User: gabriel.jabud

gravatar for gabriel.jabud
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5 months, 3 weeks ago
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5 years, 11 months ago
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Posts by gabriel.jabud

<prev • 13 results • page 1 of 2 • next >
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Answer: A: How To Identify The 16S Rrna Gene Sequence In A Genome
... For people finding this now, there is also [Barrnap][1] . Not sure how it compares to RNAmmer but it's super fast and easy to use from a command line. [1]: https://github.com/tseemann/barrnap ...
written 11 months ago by gabriel.jabud30
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Comment: C: DESeq2 (or EdgeR) Exploratory Analysis with no Replicates
... I didn't design the experiment, I inherited the data from a previous researcher and want to make use of it. I did read the edgeR manual and I will try to generate useful figures from that next. I guess I should have restated my original question as "How do I view logfold changes vs a control sampl ...
written 12 months ago by gabriel.jabud30
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Comment: C: DESeq2 (or EdgeR) Analysis with no Replicates
... Do you have a particular thread in mind? I have looked at all those pages pretty extensively and none really cover what I'm looking for. ...
written 12 months ago by gabriel.jabud30
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Comment: C: DESeq2 (or EdgeR) Analysis with no Replicates
... Yes so I can make heatmaps from the log normalized counts and do things like PCA (and I have). My question is more about what other analysis I can do and how I can compare everything to the control sample in DESeq2. For example, say I want a list of most differentially expressed genes vs control s ...
written 12 months ago by gabriel.jabud30
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Comment: C: Checking regions with high density of SNPs
... Try using IGV software (https://software.broadinstitute.org/software/igv/download) or if your lab/company will pay for it, Geneious (https://www.geneious.com/). You should be able to visualize the SNPs in IGV once you generate your .genome file (or find it online) and have a VCF file. ...
written 12 months ago by gabriel.jabud30
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DESeq2 (or EdgeR) Exploratory Analysis with no Replicates
... My pipeline so far is ```hisat2->featureCounts->DESeq2```. I have generated heatmaps after rlog and log2 transformation of the genes with the most variance, which is somewhat meaningful. What I really want to do is compare everything to the control sample and take the genes with the most log ...
deseq2 edger rna-seq written 12 months ago by gabriel.jabud30 • updated 8 months ago by Konstantinos Yeles110
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Comment: C: Is Kallisto Sleuth pipeline suitable for all organisms?
... How would you then add annotations to the Kallisto file following a Trinity de-novo assembly? ...
written 13 months ago by gabriel.jabud30
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Prokka Annotation for Bacterial Transcriptomes
... Can Prokka be used to annotate bacterial transcriptomes? Say I have a fasta file generated from a de novo assembly (Trinity). Will using Prokka the same way you annotate genomes work correctly? I don't see any mention of transcriptomes in the Prokka documentation, but it seems like it should work ...
trinity bacteria prokka annotation written 13 months ago by gabriel.jabud30 • updated 13 months ago by natasha.sernova3.7k
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Variant Calling between Microbial Populations
... I was wondering if anyone knew the caveats to doing variant calling on populations of microbes? We have whole genome sequences for several populations that were sequenced. Each population is a single strain. We would like to compare variants across these different populations. They are populatio ...
populations snp calling variant samtools written 14 months ago by gabriel.jabud30
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Is there a way to run RAST annotation locally?
... Is there any way to run RAST locally? We have found issues with using Prokka to annotate bacterial genomes and would like to give RAST a try. However, since these genomes are proprietary I can't upload them to the RAST server. Is it possible to download RAST and run it from a command line without ...
annotation rast local prokka bacterial written 14 months ago by gabriel.jabud30

Latest awards to gabriel.jabud

Teacher 6 months ago, created an answer with at least 3 up-votes. For A: How To Identify The 16S Rrna Gene Sequence In A Genome
Popular Question 5.8 years ago, created a question with more than 1,000 views. For Are there any "complete" VCF files for tomato available?
Popular Question 5.8 years ago, created a question with more than 1,000 views. For SNP and In/Del Counting without Raw Sequence Data

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