Question: Tutorial RNASEQ problem again!
0
gravatar for psschlogl
11 months ago by
psschlogl30
psschlogl30 wrote:

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

rna-seq R • 360 views
ADD COMMENTlink modified 11 months ago • written 11 months ago by psschlogl30
3

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.

ADD REPLYlink written 11 months ago by genomax83k

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

ADD REPLYlink written 11 months ago by psschlogl30
1

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

ADD REPLYlink written 11 months ago by RamRS27k

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

ADD REPLYlink written 11 months ago by psschlogl30
2
gravatar for psschlogl
11 months ago by
psschlogl30
psschlogl30 wrote:

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

ADD COMMENTlink modified 11 months ago • written 11 months ago by psschlogl30
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