User: tg369

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tg36910
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United Kingdom
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2 weeks, 6 days ago
Joined:
2 years, 6 months ago
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Posts by tg369

<prev • 17 results • page 1 of 2 • next >
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Answer: A: Nugen adapter in RNA seq
... Can STAR do that? ...
written 15 months ago by tg36910
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Nugen adapter in RNA seq
... I received RNA seq files (.fq) and I was told that the sequencing facility used Nugen (Ovation RNA-Seq Systems 1–16) kit for library prep. The seq was a directional and paired end.  Can anybody tell me where can I find adapter sequence. and how can I trim these adapters using Trimmomatic?   ...
rnaseq written 15 months ago by tg36910
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Answer: A: Scaling before normalisation in RNASeq
... Dear All, I did down sampling of reads for the outlier sample. Cluster diag generated after normalisation, using normalised raw counts, looks like the outlier issue is resolved. However, that was bit confusing.  Therefore,  I performed PCA; also generated a heat map by taking 1000 highly variable g ...
written 2.4 years ago by tg36910
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Answer: A: Scaling before normalisation in RNASeq
... Thank you b.nota, Aaron Lun, Gordon Smyth and Hans-Rudolf for discussing this issue and your advice and suggestions. We plan to repeat these experiments. However, in the meantime, I just try to select reads randomly and let us see the result. Will let you know as soon as I have my result.  Tanay   ...
written 2.4 years ago by tg36910
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Scaling before normalisation in RNASeq
... I have one sample that we ran for sequencing separately and having more coverage and more reads. At the end this sample is coming as an outlier when I prepared a cluster diagram. This problem still persist after I did normalisation (DESeq method). This can be biological reason, but we also suspect ...
normalization written 2.4 years ago by tg36910
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STAR_how many mismatches to allow if the read length is 100 bp in RNA-seq data
... Hi, I have 100bp reads (single end) and want to align with the mouse genome using STAR. How do I decide how many miss-matches I should allow? or Should I run STAR in default (where upto 10 miss-matches are allowed in default mode). I will highly appreciate your advice. Many thanks in advance. Ki ...
star written 2.5 years ago by tg36910
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Comment: C: DESeq2_multiple correction_no significance
... Hi Michael, I refer to our discussion for using trim mean filtering. My specific question is that running apply(counts(dds, normalized=TRUE), 1, mean, trim=1/6) after dds <- estimateSizeFactors(dds) and then doing dds<-DESeq(dds) would automatically filter genes?  or I am really missing some ...
written 2.5 years ago by tg36910
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Answer: A: DESeq2_Error in .call2, what does it mean?
... Thank you Mike. That was the case. doing updateObject (dds) fixed the problem. ...
written 2.5 years ago by tg36910
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DESeq2_Error in .call2, what does it mean?
... I was running DESeq2. However after running DESEq() I got the following: > dds<-DESeq(dds); using pre-existing size factors estimating dispersions gene-wise dispersion estimates Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") :    solving row 463827: negative widths ...
deseq2 written 2.5 years ago by tg36910
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Comment: C: Fraction arguments for multi mapping reads in featureCounts in Rsubread
... Many thanks Gordon and Wei,  that is working now after updating R version. ...
written 2.5 years ago by tg36910

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Popular Question 15 months ago, created a question with more than 1,000 views. For Fraction arguments for multi mapping reads in featureCounts in Rsubread

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