User: fa.gholizadeh89

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Posts by fa.gholizadeh89

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Could an experienced user of Polyester help me with some questions?
... Hi, I'm highly in need of simulating a count matrix. I have read the manual and vignette of Polyester several times but I find it very confusing. The problem I'm gonna solve using Polyester is that I have a count matrix of 4 replicates in 4 time points from a real experiment. This is a time course ...
time course rna-seq polyester simulation written 23 months ago by fa.gholizadeh890
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Comment: C: How to simulate a count matrix using Polyester
... Thank you very much. I try to apply it. But from the manual, it says that the output is the fasta files ("create FASTA files containing RNA-seq reads simulated from provided transcripts, with optional differential expression between two groups (designated via read count matrix)"). does it mean that ...
written 23 months ago by fa.gholizadeh890
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How to simulate a count matrix using Polyester
... Hi, I'm gonna simulate some RNA-seq read counts data from a real data set for publication purposes. My problem is I can't download big Fasta files. So I want to obtain the count matrix using galaxy and then simulate data using that count matrix. There are some R packages such as SimSeq and Polyeste ...
rna-seq count matrix polyester simulation written 23 months ago by fa.gholizadeh890 • updated 23 months ago by Alyssa Frazee210
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Comment: C: high number of DEGs detected using EBSeq-HMM *****UPDATED
... Could a problem be that there are some uncontrolled batch effects in data which could lead to these strange results? They themselves have used a non-standard normalization method to adjust for the batch effects but I didn't adjust for the batch effects and I only controlled the sequencing depth bias ...
written 2.7 years ago by fa.gholizadeh890
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Comment: C: high number of DEGs detected using EBSeq-HMM *****UPDATED
... It's a real data set. I downloaded it from ncbi. These are the genes found by default settings of each model (only the adj.P.value) and I haven't filter them by FC or further analysis. ...
written 2.7 years ago by fa.gholizadeh890
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Comment: C: high number of DEGs detected using EBSeq-HMM *****UPDATED
... Thank you for your response. I have 4 time points and 4 replicates at each time point. Other models identify about 10k to 12k genes by default. I wanna compare two models with a benchmark model to investigate which one is doing better at detecting DEGs. So all I need to know is that is it ordinary t ...
written 2.7 years ago by fa.gholizadeh890
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high number of DEGs detected using EBSeq-HMM *****UPDATED
... Hi, I'm using EBSeq-HMM to find DE genes. The problem is among 17611 genes, 16139 genes are identified as DE which is very unusual. My cutoff to filter genes out before detecting DE genes was to discard all those genes without at least 5 reads in at least one sample. Do you think my result is ok? ...
ebseq-hmm written 2.7 years ago by fa.gholizadeh890

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