User: Laura.Fancello

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Posts by Laura.Fancello

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riboSeqR: interpret plots generated by plotTranscript function
... Hi, I am using riboSeqR for framshift analysis on ribosome profiling data. I obtained alignments for individual transcripts using the riboSeqR plotTranscript function. However it is not clear to me how to interpret these plots. Let's take for example Figure 3 at page 5 of the riboSeqR reference ma ...
riboseqr plottranscript function written 4.7 years ago by Laura.Fancello0
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Comment: C: RiboSeqR package input file format
... Dear Thomas thanks for your answer. I still have some questions about riboSeqR: In the filterHits function the option hitMean is not really clear to me. I understood that a minimum number of reads (ribosome footprints) for ONE coding region are required to consider that coding region translated. I ...
written 4.7 years ago by Laura.Fancello0
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RiboSeqR package input file format
... Hi, I want to use the riboSeqR package on the output of a TopHat mapping but I have problems getting the right format for this file. My file looks like this: @HD VN:1.0 SO:coordinate @SQ SN:chr1 LN:249250621 @SQ SN:chr10 LN:135534747 @SQ SN:chr11 LN:135006516 @SQ ...
riboseqr written 4.7 years ago by Laura.Fancello0 • updated 4.7 years ago by Thomas J Hardcastle180
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DESeq2 independent filtering using filter=rv
... Hi, I'm using DESeq2 for DE analysis. I found in the "Beginner's guide to the "DESeq2" that it's possible to perform both default independent filtering (which uses mean of normalized counts as a filter statistics) and independent filtering with other filters, such as filter=rv. Could you please expl ...
deseq2 independent filtering written 4.8 years ago by Laura.Fancello0 • updated 4.8 years ago by Michael Love24k

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Popular Question 4.4 years ago, created a question with more than 1,000 views. For DESeq2 independent filtering using filter=rv

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