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How to know which samples are treated and untreated?

untreated colorectalcancer treated written 2.1 years ago by bio94 • 50 • updated 2.1 years ago by Santosh Anand ♦ 5.1k

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From cuffmerge to cuffdiff: What input for cuffdiff?

controls cuffdiff rna-seq cuffmerge treated written 4.2 years ago by YaGalbi • 1.5k • updated 4.2 years ago by onspotproductions • 140

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Recent Replies

C: Variant Call Format (.vcf) conversion to .bam by Hamid Ghaedi • 220
Upvoted your answer because I supposed, @abyssaldharok has not idea about what he/she asked.
C: Difference in imputation between platforms and RS names by Kevin Blighe ♦ 65k
I suppose that it indicates how disagreement is on rare alleles; so, the differences could be acc...
A: No color observed in Colour Key of HeatMap.2 by morty • 0
Hi, It is likely because of this line: col1 <- colorRampPalette(c("green", "black", "red"))(4...
A: Variant Call Format (.vcf) conversion to .bam by swbarnes2 ♦ 8.6k
To quote another poster in these parts, what you are asking is like asking how to turn a steak in...
C: Differential Abundance Analysis wih DESeq2 and metabolites as continuous predict by greenm11 • 0
Hi, Sorry I should have made it more clear: I repeat this process for each timepoint that has i...
C: testing set for RNA-seq AML by Ali • 0
Thanks for your reply I use TCGA data was fine to download and run the analysis where the sampl...
C: empty fastq files created by docker bcl2fastq2 v2.20 OSX by akh22 • 40
The input folder appears to be intact, containing everything original except the samplesheet.csv...
C: how to split M3VCF by ID? by Pierre Lindenbaum ♦ 130k
I had to google for m3vcf: https://genome.sph.umich.edu/wiki/M3VCF_Files > is there an automa...
C: Difference in imputation between platforms and RS names by anamaria • 100
it seems that characteristics of overlapping SNPs is that there is not many of them who have very...
C: testing set for RNA-seq AML by newbio17 • 230
Have you tried [GEO][1] or [cBioPortal][2] to see if they have any dataset you could use? [1]...
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If you want another method of checking for rRNA to double check, you can try `split_bam.py` from ...
C: Transcriptome analysis of two closely related plant species by Istvan Albert ♦♦ 84k
yes, you can split a bam file by chromosome, and spawn a separate process with gnu parallel

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