User: tunl

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tunl50
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Posts by tunl

<prev • 71 results • page 1 of 8 • next >
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Comment: C: RNA-seq long reads vs. transcripts
... Thanks so much! So this means we would have to run an assembler on the long reads in order to automatically get transcripts in GFT from them (or are there some other automated ways to do so?). However, as I found out that different assemblers got quite different outputs from the same long read datas ...
written 12 months ago by tunl50
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Comment: C: RNA-seq long reads vs. transcripts
... This is great information! Thank you so much for your advice! I’ll look into this paper. Thanks a lot! ...
written 12 months ago by tunl50
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Comment: C: RNA-seq long reads vs. transcripts
... Thank you very much for your advice! I was wondering if there are some ways to get transcripts (in GTF format) from long reads instead of running assemblers on them? I tried running different assemblers on the same long-read dataset (PacBio) and got very different results (some assembler outputs mu ...
written 12 months ago by tunl50
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RNA-seq long reads vs. transcripts
... Long reads technologies claim that their RNA-seq long reads are full-length transcripts, so transcript assembly is no longer needed. I am wondering what may be the differences between long reads and transcripts: are they truly equivalent? If I want to get transcripts (in GTF format) from long read ...
assembly long reads rna-seq written 12 months ago by tunl50
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Comment: C: A question about differential expression analysis
... Thank you so much Devon! This is great info and advice! ...
written 15 months ago by tunl50
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A question about differential expression analysis
... My understanding is that most differential expression analysis tools for RNA-seq (bulk or single-cell) use negative binomial distribution, while some use the likelihood ratio test. Would it be possible to do a simple t-test for differential expression analysis of single-cell RNA-seq data? Thank y ...
single-cell rna-seq de analysis rna-seq written 15 months ago by tunl50 • updated 15 months ago by Devon Ryan88k
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Comment: C: Differential expression analysis tool for single cell RNA-seq data
... Thanks so much for the information! ...
written 16 months ago by tunl50
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Comment: C: Differential expression analysis tool for single cell RNA-seq data
... This is great! Thank you so much! Monocle vs. MAST, which one do you think is better? Thanks a lot! ...
written 16 months ago by tunl50
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Differential expression analysis tool for single cell RNA-seq data
... I am looking for the best available differential expression analysis tool for single cell RNA-seq data. From the literatures that did some comparisons, I found that MAST, ROTS, SCDE, DEGseq, D3E, and SAMseq seem to have good performance. Which one would you recommend based on your actual experience ...
single-cell rna-seq de analysis rna-seq written 16 months ago by tunl50 • updated 16 months ago by theobroma221.1k
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Comment: C: Length distribution of PacBio RNA-seq
... It used polyA RNA. Thanks a lot! ...
written 17 months ago by tunl50

Latest awards to tunl

Popular Question 15 months ago, created a question with more than 1,000 views. For Read pairing issues detected in Tophat run
Popular Question 23 months ago, created a question with more than 1,000 views. For Coverage-search vs. no coverage-search in running Tophat
Supporter 2.6 years ago, voted at least 25 times.

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