User: lkianmehr

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lkianmehr30
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France
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Posts by lkianmehr

<prev • 74 results • page 1 of 8 • next >
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Comment: C: gene ontology analysis based on transcript biotype
... could you please make some example of those specialized databases annotate gene ontology or functional terms from lncRNAs as well and which stage you recommend to separate protein_codings before DGE analysis or doesn't matter if done after that? ...
written 4 weeks ago by lkianmehr30
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gene ontology analysis based on transcript biotype
... I have a list of transcripts (quantified by Salmon), may I filtered them out based on biotype, for instance, protein_codings or lncRNA, then do GO for each one separately? ...
biotype gene ontology transcript written 4 weeks ago by lkianmehr30 • updated 4 weeks ago by EagleEye6.2k
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how do normalization for transcript length
... I have got transcript quantification by Salmon, then import them to tximport and got transcript count, length and abundances. now I would like to make a transcript coverage graph in terms of normalized counts on normalized position along transcript. I have normalized counts by DESeq2 but I don't kno ...
tximport transcript coverage salmon plot written 4 weeks ago by lkianmehr30
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Comment: C: Gene Set Clustering based on Functional annotation (GeneSCF)
... geneSCF-master-source-v1.1-p2 ...
written 4 weeks ago by lkianmehr30
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Comment: C: Gene Set Clustering based on Functional annotation (GeneSCF)
... I have tried to do GO with genescf as I did for the same gene symbols list by DAVID, but results with genescf are very different, and no P-values is significant (based on EASE less than 0.05). need to mention that I have used mgi as -db. DO you have any idea about this conflict? ...
written 4 weeks ago by lkianmehr30
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some questions to do GO enrichment analysis
... Hello, I have a list of MOUSE genes (from RNA-seq analysis) include 800 up and 7150 down regulated from DESeq2 . I did GO enrichment analysis for up-regulated genes by DAVID, and got 3 list of functional groups (84 GO term for Molecular function, 57 GO term for cellular component and 163 Go term f ...
mouse gene ontology rna-seq written 5 weeks ago by lkianmehr30 • updated 5 weeks ago by EagleEye6.2k
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Comment: C: how to get percent identity between two RNA-seq fastq files?
... I have run that command on two fastq files that are sequenced on the same library, I got one value = 0.119817, what does it mean? it means they have just 0.1 percent difference? ...
written 8 weeks ago by lkianmehr30
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how to get percent identity between two RNA-seq fastq files?
... Hello, Does anybody have an idea about the way to get percent identity between two or more RNA-seq fastq files ? or to show how many of the sequences in one of them are found in another one? thanks in advance ...
percent identity rna-seq written 8 weeks ago by lkianmehr30 • updated 8 weeks ago by Pierre Lindenbaum116k
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Comment: C: May I use numreads for doing DGE after quantifying by Salmon
... but I taught that tximport should be used just for summarizing transcript_id to gene_id ...
written 3 months ago by lkianmehr30
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May I use numreads for doing DGE after quantifying by Salmon
... Hello, I have quantified piRNA and tRNA of RNA-seqs by Salmon on fasta file, now to do DGE analysis may I use numreads ? ...
salmon dge written 3 months ago by lkianmehr30 • updated 3 months ago by WouterDeCoster36k

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