User: rthapa

rthapa • 0

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Posts by rthapa

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218

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txt files of upregulated and down regulated genes

... Hi, My apology if it appears to be a silly question. I wanted to save the files of upregulated and downregulated genes from DESeq2. But both of my files have lfc value of both positive and negative. I think the upregulated genes should have positive lfc value and downregulated genes should have nega ...

rna-seq written 5 months ago by rthapa • 0 • updated 5 months ago by WouterDeCoster ♦ 29k

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296

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best value of lfc threshold

... What is the best value to assign for lfc threshold while using DESeq2 package? With 1 as lfc threshold, I got more than 3000 upregulated genes. Any suggestion please? Thanks ...

rna-seq written 5 months ago by rthapa • 0 • updated 5 months ago by Kevin Blighe ♦ 21k

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240

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DESeq2 lfc shrinkage

... Hi! How can we determine the coefficient value while applying lfcShrink() with the coefficient argument? Thanks ...

rna-seq written 5 months ago by rthapa • 0

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237

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truncated bam file

... Hi! I have got a sam file which looks good but when I convert it to bam file, the file became truncated. The tail of bam file looks weird. Could anyone suggest me what could be the reason? Thanks ...

rna-seq written 5 months ago by rthapa • 0 • updated 5 months ago by Jean-Karim Heriche ♦ 15k

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270

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transcript count after string tie merge

... Hi, I am trying to get transcript counts with stringtie merge command. I have set of gtf output, when I checked the transcript counts of individual gtf files, I got some values of transcript counts but when I used strigtie merge command to merge all the stringtie files, I got merged output file but ...

stringtie rna-seq written 5 months ago by rthapa • 0 • updated 5 months ago by Kevin Blighe ♦ 21k

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