Hi guys I trying to get experience in R and RNASEQ analysis and time to time I get some trouble find out some data. I am following this tutorial
However I got stucked here:
library(dplyr) sraInf <- mutate(sraInf, bam=paste0(run, ".sorted.bam")) gseInf <- mutate(gseInf, experiment = basename(as.character(supplementary_file_2)), newbam = gsub("Sample name: ","", description), newbam = gsub("-",".",newbam,fixed=TRUE), newbam = paste0(newbam, ".bam")) gseInf
I got a error msg:
Error: Evaluation error: object 'supplementary_file_2' not found.
I tried to find that file in the results of
sraInf, but just find a
I didn't used R to download the files but SRA tool kit.
I did get the results using file 1, but the names got some creep:
1 GSM1480291_MCL1-LA_BC2CTUACXX_GATCAG_L001_R1.txt.gz MCL1.LA.bam 2 GSM1480292_MCL1-LB_BC2CTUACXX_TGACCA_L001_R1.txt.gz MCL1.LB.bam 3 GSM1480293_MCL1-LC_BC2CTUACXX_GCCAAT_L001_R1.txt.gz MCL1.LC.bam 4 GSM1480294_MCL1-LD_BC2CTUACXX_GGCTAC_L001_R1.txt.gz MCL1.LD.bam 5 GSM1480295_MCL1-LE_BC2CTUACXX_TAGCTT_L001_R1.txt.gz MCL1.LE.bam 6 GSM1480296_MCL1-LF_BC2CTUACXX_CTTGTA_L001_R1.txt.gz MCL1.LF.bam 7 GSM1480297_MCL1-DG_BC2CTUACXX_ACTTGA_L002_R1.txt.gz MCL1.DG.bam 8 GSM1480298_MCL1-DH_BC2CTUACXX_CAGATC_L002_R1.txt.gz MCL1.DH.bam 9 GSM1480299_MCL1-DI_BC2CTUACXX_ACAGTG_L002_R1.txt.gz MCL1.DI.bam 10 GSM1480300_MCL1-DJ_BC2CTUACXX_CGATGT_L002_R1.txt.gz MCL1.DJ.bam 11 GSM1480301_MCL1-DK_BC2CTUACXX_TTAGGC_L002_R1.txt.gz MCL1.DK.bam 12 GSM1480302_MCL1-DL_BC2CTUACXX_ATCACG_L002_R1.txt.gz MCL1.DL.bam
I don't know if any of you did this tut? I don't know if I could go along with these names of files or If any of you did this tut
were did you got that missing file? (
Thanks for any direction.