Question: tximeta error (coldata)
0
gravatar for eridanus
5 weeks ago by
eridanus10
eridanus10 wrote:

Hello. I am trying to use tximeta package. I have quant.sf files from salmon. my code is the following one:

dir <- "/home/quant_sf"
names<-c("28","29","30","31","32","33","34","35","36","37","38","39")
files <-file.path(dir, names,"quant.sf")
files
file.exists(files)
coldata <- data.frame(files,names=names, stringsAsFactors=FALSE)
coldata
se <- tximeta(coldata)

I am getting the following error: Error: lexical error: invalid char in json text.
                                      /home/quant_sf
                     (right here) ------^

Could someone help me? Thank you so much in advance!!

rna-seq R • 147 views
ADD COMMENTlink modified 4 weeks ago by LabCoatNomad10 • written 5 weeks ago by eridanus10
1

I think I see the problem with your code BUT even when corrected I didn't get the desired output from tximeta

I ended up just using quantmerge to combine my salmon outputs and imported that as a count matrix because it was way easier.

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by LabCoatNomad10
1

Then use tximport. It does the exact same except it does not add the metadata which are (imho) mostly not necessary for a standard analysis. tximeta seems a bit overloaded to me right now, and this annoying json dependency is one of the factors it is currently unattractive compared to tximport which is super easy to use. Also, quantmerge does not aggregate to the gene level so this is not really a workaround afai can see.

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by ATpoint42k

Now I am trying to use tximport. However I am having a hard time creating tx2gene. I have used gencode.v33.transcripts.fa.gz and Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz for indexing. Any thoughts? Thank you!

ADD REPLYlink written 4 weeks ago by eridanus10

could you tell me the error in my code? thanks!!

ADD REPLYlink written 4 weeks ago by eridanus10

quant_sf is a folder containing 12 more folders -named as names vector- (each folder contains 1 quant.sf file). So for example: /home/quant_sf/28/quant.sf is the full path.

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by eridanus10
1

I remember that I also had that error and was annoyed by it, and simply used tximport. Suggest to ask this over at support.bioconductor.org so the developer can have a look. Please include output of sessionInfo() if you do.

ADD REPLYlink written 4 weeks ago by ATpoint42k

thank you so much for your reply!i will try tximport..

ADD REPLYlink written 4 weeks ago by eridanus10
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