Help regarding DESeq2
1
0
Entering edit mode
@7ca586f4
Last seen 2 days ago
India

Respected sir, Currently, I am working on chicken ovarian transcriptomics data analysis. Since I am new to this, I am following your previously published paper (Beginner’s guide to using the DESeq2 package) for analysing my data. So far I have followed few steps which I have mention below. Further, I don't know which steps I have to follow. If you help, it will be greatly helpful for me.

Sincerely KAMALAKKANNAN R

Note:

library("DESeq2")
library("GenomicFeatures")
chicken <- makeTxDbFromGFF("F:/ChickenTranscrptomics data analysis/Chicken/Gallus.gff", format="gff")
exonsByGene <- exonsBy(chicken, by="gene")
fsl <- list.files("F:/Duck Transcrptomics data analysis/Chicken/BAM", pattern="bam$", full=TRUE)
library("Rsamtools")
bamLt <- BamFileList(fsl, yieldSize=100000)
library("GenomicAlignments")
kamal <- summarizeOverlaps(exonsByGene, bamLt, mode="Union", singleEnd=TRUE, ignore.strand=TRUE, fragments=FALSE)
colData(kamal)
rowData(kamal)
tail(assay (kamal))
head(assay (kamal))
sample <- read.csv("F:/ChickenTranscrptomics data analysis/Chicken.csv")
head( sample )
head( colnames(kamal) )
sample1 <- DataFrame(sample)
sample1
id <- match(colnames(kamal), sample1$run)
id
head( cbind( colData(kamal)[, 1:2 ], sample1 [ id, ] ) )
colData(kamal) <- cbind( colData(kamal), sample1[ id, ] )
DESeq2 • 115 views
ADD COMMENT
0
Entering edit mode
@mikelove
Last seen 2 days ago
United States

On the support site I can provide specific software issues related to DESeq2, if you have a need for general bioinformatic support, I suggest you reach out to a bioinformatic collaborator.

The workflow and vignette both provide detailed documentation and guidance.

ADD COMMENT

Login before adding your answer.

Traffic: 463 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6