User: Dennis

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Dennis10
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Posts by Dennis

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Comment: C: I am slightly confused about the input requirements for the differential express
... Hello Dennis! We believe that this post does not fit the main topic of this site. Reposted at another forum For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with. If you disagree please tell us why in a reply below, ...
written 10 weeks ago by Dennis10
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Comment: C: I am slightly confused about the input requirements for the differential express
... Thank you Jen, I'll repost this where suggested, but DESeq2 wasn't working for me with TPM reads if you remember, there is a bug. I'm still trying to resolve what it needs as an input as I tried "feeding" it all sorts of TPM input tables, but fortunately found someone who may help me run Deseq2 in ...
written 10 weeks ago by Dennis10
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Comment: C: I am slightly confused about the input requirements for the differential express
... Thanks Jen! Is there a way to TMM-normalize using R or Excel? Cheers, Dennis ...
written 11 weeks ago by Dennis10
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(Closed) I am slightly confused about the input requirements for the differential expression tool - last step of Trinity
... Hello all, I have a pressing question... To start with, I have read the Trinity methods paper and Googled TMM normalization and different unit format prior to asking this question here: I have a paired ends RNAseq data set with 3 conditions and 3 replicates. I have assembled a transcriptome de ...
galaxy rna-seq written 11 weeks ago by Dennis10 • updated 11 weeks ago by Jennifer Hillman Jackson23k
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Answer: A: Fatal error with DESeq2 when processing TPM-based Salmon files and using a tabul
... Hi Jen, This was my first suspect so I removed all the spaces and merged all the columns into one producing a one long name, no spaces or any non-alphanumeric characters for the gene ID. Now the tool runs, but comes back empty :-/ All three files: normalized counts, plots and files on data are e ...
written 12 weeks ago by Dennis10
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Comment: C: salmon gene quant to DESeq2
... Hi Matthew, Have you resolved this issue? I've run into similar problems with my use of DESeq2 on Salmon files and TPM input coupled with a transcript-ID gene-ID mapping file. ...
written 12 weeks ago by Dennis10
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Fatal error with DESeq2 when processing TPM-based Salmon files and using a tabular transcript-gene mapping file
... Hi there, I have used Salmon to map RNAseq reads to a transcriptome. I then proceeded to analyze Salmon output with DESeq2: - choice of input data: TPM values (e.g., from salmon) - transcript-ID and gene-ID mapping file (tabular file with transcript-gene mapping) I used a tabular text file tha ...
software error rna-seq written 12 weeks ago by Dennis10
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Comment: C: Can a genome that's been released be added so I can map against it
... Hi Jen, Thank you so much - I'll try to work through this. I already normalized all the FASTA files and clipped the title lines at the first white space, but they don't seem to match the GFF file - I downloaded the normalized contigs and they have names like >tig000033_pilon while the GFF file w ...
written 12 weeks ago by Dennis10
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Answer: A: Can a genome that's been released be added so I can map against it
... Hello again, The recommended guide for adding a custom genome asks to "Make sure the chromosome identifiers are a match for other inputs". In the data I have access to (link above), I can't find any chromosome identifiers. Scaffolds contigs files contain names only followed by sequences in fast fo ...
written 12 weeks ago by Dennis10
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Comment: C: Can a genome that's been released be added so I can map against it
... Thank you! Let me try to walk through this process! Should I upload contains or scaffolds in FASTA to map my reads to? Thanks again, Dennis ...
written 12 weeks ago by Dennis10

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