Biostar Tophat

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snpeff python tophat r RNAseq123

updated 15 hours ago by Kevin Blighe 3.2k • written 15 hours ago by kusum • 0

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245

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noiseq rsubread tophat bowtie bowtie2

2.1 years ago Marcelo Laia ▴ 440

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406

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topGO tophat kolmogorov-smirnov test

updated 4.0 years ago by James W. MacDonald 57k • written 4.0 years ago by aaronrosenstein • 0

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1.0k

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R rnaseq tophat summarizeoverlaps systempiper

updated 4.7 years ago by Thomas Girke ★ 1.7k • written 4.7 years ago by abass.conteh • 0

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5.7k

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deseq deseq2 edger tophat bowtie

6.1 years ago ysdel ▴ 40

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1.5k

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rnaseq summarizeOverlaps deseq2 tophat genomicalignments

updated 6.7 years ago by Dan Tenenbaum ★ 8.2k • written 6.7 years ago by alejandro.colaneri ▴ 20

6 results • Page 1 of 1

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Comment: Best practice for quantifying sncRNA by Abhishek • 0

k has to be odd - trying 9, 21 instead

Comment: Best practice for quantifying sncRNA by Abhishek • 0

I did use the genome as decoy. And I used whole transcriptome from Gencode for indexing. Maybe I should index using just non coding transc…

Comment: Best practice for quantifying sncRNA by Abhishek • 0

Thank you for your suggestions. Throwing away larger reads sounds true, I'll try using Cutadapt for that besides adapter trimming. I did …

Comment: Best practice for quantifying sncRNA by Abhishek • 0

Thanks, I will try out Bowtie. Is GeneGlobe and Qiagen the same company ? https://www.qiagen.com/us/resources/download.aspx?id=bea2dcfa-…

Answer: Using both spike in and TMM normalizations in ChIP-seq samples by Gordon Smyth 43k

It is impossible to use both spike-in or TMM normalization. You must do one or the other. They replace each other, they cannot be combined.…

Votes

Comment: Idea: Using DESeq2 to test a change in ratio of two genes

Time Series Analysis

Comment: Time series DE gene analysis with edgeR where specific timepoints have NA levels

Answer: Time series DE gene analysis with edgeR where specific timepoints have NA levels

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Teacher to JP Carter ▴ 40