User: gabriel.jabud

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Posts by gabriel.jabud

<prev • 12 results • page 1 of 2 • next >
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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 8 days ago by gabriel.jabud0
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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 8 days ago by gabriel.jabud0
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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 8 days ago by gabriel.jabud0
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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 8 days ago by gabriel.jabud0
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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 8 days ago by gabriel.jabud0
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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 19 days ago by gabriel.jabud0
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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 26 days ago by gabriel.jabud0 • updated 26 days ago by natasha.sernova3.4k
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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 7 weeks ago by gabriel.jabud0
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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 9 weeks ago by gabriel.jabud0
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Mauve alignment vs samtools for SNP calling
... If I have two assembled genomes (one reference), what is the difference between doing SNP calling using something like Samtools from the raw Illumina reads and doing a Mauve alignment after assembly of each genome? Would Samtools be much more accurate? It seems easier to just do a Mauve alignment ...
snp calling alignment samtools snp mauve written 10 weeks ago by gabriel.jabud0 • updated 10 weeks ago by jrj.healey12k

Latest awards to gabriel.jabud

Popular Question 4.8 years ago, created a question with more than 1,000 views. For Are there any "complete" VCF files for tomato available?
Popular Question 4.8 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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