Tutorial RNASEQ problem again!

Question

[psschlogl]

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 supplementary_file_1.

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? (supplementary_file_2)

Thanks for any direction.

Paulo

[GenoMax]

A quick perusal of the GitHub site does not immediately show that specific file being present. You may need to contact the authors by creating an issue here.

[psschlogl]

I did check it out already 8 ( I will try to found it out with the autors. Thanks

[Ram]

Is there some way you could contact the authors of the tutorial? They'd be able to answer your question most accurately.

[psschlogl]

I will check it out but I not sure they will be quick as you guys here! Thanks

Answer 1

[psschlogl]

Just to let you know, I figured out. In my case I had a supplementary file 1. So I just got the results changing 2 for 1.

Anyway

Thank you guys! You rock!

See ya