User: thindmarsmission

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Posts by thindmarsmission

<prev • 11 results • page 1 of 2 • next >
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Comment: C: which normalized counts is better from DESeq2
... I am curious to know, while obtaining normalized count from "`count(dds, normalized=T)`", Does design provided from folloiwing command has an effect on normalized count? dds <- DESeqDataSetFromMatrix(countData = x, colData = ss.edesign, design = ~Condition) ...
written 5 weeks ago by thindmarsmission0
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Comment: C: How To Extract Spliced Rnaseq Reads
... Is it possible to count spliced read over intron from intron.bed? ...
written 6 weeks ago by thindmarsmission0
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Comment: C: Counting reads supporting a specific splice junction from bam file
... What is the possible way, to count the spliced reads (over introns). I want to count it for all the introns. Is there any method to extract that information from IGV? I can see in sashmi plot, it shows the spliced read count for each intron. ...
written 6 weeks ago by thindmarsmission0
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Comment: C: 5', 3' SS and Intron retention read count using STAR out.tab
... Thanks for suggestion. I am just trying out this tool. Do you think, I can find Intron retention events using this tool? ...
written 7 weeks ago by thindmarsmission0
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5', 3' SS and Intron retention read count using STAR out.tab
... Hi! I am interested in the study of alternative splicing sites 5 and 3 and Intron retenton. I just want it, in the form of read count that how many numbers of reads and percentage of reads/total coverage reads, belongs to one splice site and same thing for other site. NOTE: I don't have two diffe ...
star rna-seq alternative splicing written 7 weeks ago by thindmarsmission0
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reliability for the usage of merged GTF from tophat-cufflinks as an novel annotation?
... Hi! I want to study alternative splicing events between two different conditions using RNA-seq data of new paramecium strain [lets say "A"]. I want to use MATS for this using merged gtf annotation from tophat and cufflinks, which is based on reference and annotation(GFF3) of another closed related s ...
cufflinks mats rna-seq alternative splicing written 7 weeks ago by thindmarsmission0 • updated 5 days ago by Biostar ♦♦ 20
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Comment: C: Signature genes from RNA-seq time series (Developmental)
... I have similar question, did you find the answer for this? If yes, please update. ...
written 10 weeks ago by thindmarsmission0
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Answer: A: How to export the output list of csCluster( ) from CummeRbund?
... `enter code here`to export the list of cluster and corresponding gene list : clusterinfo=ic[["clustering"]] write.table(clusterinfo2,"file.tsv", sep="\t") ...
written 10 weeks ago by thindmarsmission0
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design matrix for time point comparision [1 treatment] in time course RNA Seq - EdgeR
... HI! I am trying to analyse Time course data with just one type cell (3 biological replicate ) for each point . I want to compare gene expression based on time point i.e time 1 with time 2 and so on (no treatment comparision at different points, becuase it's one type only). So what I prepared so fa ...
rna-seq edger masigpro written 12 weeks ago by thindmarsmission0 • updated 10 weeks ago by Antonio R. Franco3.9k
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Comment: C: Best pipeline for time course RNA-SEQ analysis for single cell organism
... Thanks, Can you please suggest any article related to my experiment conditions; means different biological replicates and time point. ...
written 3 months ago by thindmarsmission0

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