User: Lorenzo.Pavarini

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3 months, 1 week ago
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4 months, 1 week ago
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L***************@4dpharmaplc.com

Posts by Lorenzo.Pavarini

<prev • 6 results • page 1 of 1 • next >
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Answer: A: StringTie Output for DESeq analysis
... I found the solution. Among the StringTie Parameters I select yes in "Use Reference transcripts only" and in this case i got same line numbers in each file ...
written 3 months ago by Lorenzo.Pavarini20
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Creating StringTie output that meets DESeq expected input content for DE analysis
... Good Morning, Since StringTie can produce output files for differential expression that can be used by DEseq2 i would like to use it for this. But i got an error during DESeq using the tubular files produce by StringTie In my case I got 6 sample, I have run Stringtie using a GTF file as a reference ...
stringtie deseq rna-seq written 3 months ago by Lorenzo.Pavarini20 • updated 3 months ago by Jennifer Hillman Jackson25k
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DESeq2 changing name
... Good Morning, I am using DESeq2 to analyze the differential expression between 2 phase of growth of my bacteria. Everything works but I don't know why in the results (both the table and the pdf) the name of my samples is change in this type of name: X7647 StationaryXPhase X9173 StationaryXPhase X51 ...
deseq2 rnaseq written 3 months ago by Lorenzo.Pavarini20
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Comment: A: Differential Expression in bacteria RNA-seq
... Actually, I think that the problem could my in my GFF3 file. If I open it with excel it is like this ##gff-version 3 ##source-version geneious 9.1.8 MRx0004_ER_19051 Geneious CDS 1 1467 . + . ID=Chromosomal replication initiator protein DnaA CDS MRx0004_ ...
written 4 months ago by Lorenzo.Pavarini20 • updated 4 months ago by Jennifer Hillman Jackson25k
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Answer: A: Differential Expression in bacteria RNA-seq
... Good Afternoon, Right now I am trying to use the workflow by devikasub (https://usegalaxy.org/u/devikasub/w/workflow-constructed-from-history-gccworkflow-1) for the differential expression of my bacteria RNA. I follow the procedure and everything works great until **Cuffmerge**. Who give me this er ...
written 4 months ago by Lorenzo.Pavarini20 • updated 4 months ago by Jennifer Hillman Jackson25k
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Differential Expression in bacteria RNA-seq
... Hello, I got a problem in Cufflinks: I need to analyze fastq file from a RNA-seq (I got bacteria RNA),and I wuold like to use Bowtie2, Cufflinks, Cuffmerge and Cuffdiff to do the Differential Expression of 2 set of sample. I am just trying with 1 sample, The fastqc is ok Bowtie works But when I us ...
rna-seq cufflinks bacteria written 4 months ago by Lorenzo.Pavarini20

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Scholar 3 months ago, created an answer that has been accepted. For A: StringTie Output for DESeq analysis

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