DEGseq

[yueli]

Hi,

I try to use DEGseq to process my miRNA data which only have *.fasta file.

I used bowtie to alignment my 1.fa and 2.fa to the contigs.fa, then use convert2bed transform my *.sam files to *.bed files.

I made the refFlat file of miRNAs in planarian Schmidtea midterranea shown as refFlatmiR_smed.

Any suggestions are appreciated!

Li






> clean1 <- system.file("extdata", "contigs_1.bed", package="DEGseq")
> clean2 <- system.file("extdata", "contigs_2.bed", package="DEGseq")
> refFlat <- system.file("extdata", "refFlatmiR-smed", package="DEGseq")
> mapResultBatch1 <- c(clean1)
> mapResultBatch2 <- c(clean2)
> outputDir <- file.path(tempdir(), "DEGseqExample")
> DEGseq(mapResultBatch1, mapResultBatch2, fileFormat="bed", refFlat=refFlat,outputDir=outputDir, method="LRT")
Please wait...

mapResultBatch1:
/home/li/R/x86_64-pc-linux-gnu-library/2.15/DEGseq/extdata/contigs_1.bed
mapResultBatch2:
/home/li/R/x86_64-pc-linux-gnu-library/2.15/DEGseq/extdata/contigs_2.bed
file format: bed
refFlat:
Ignore the strand information when count the reads mapped to genes!
Count the number of reads mapped to each gene ...
This will take several minutes, please wait patiently!
Please wait...

SampleFiles:
/home/li/R/x86_64-pc-linux-gnu-library/2.15/DEGseq/extdata/contigs_1.bed
Count the number of reads mapped to each gene.
This will take several minutes.
Please wait ...
cannot open input file
There is something wrong!
Please check !
There is something wrong!Please check...
错误于file(file, "rt") : 无法打开链结
此外: 警告信息：
In file(file, "rt") :
无法打开文件'/tmp/RtmpOGTL8Y/DEGseqExample/group1.exp': 没有那个文件或目录