Question

tximeta error (coldata)

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3.5 years ago

eridanus ▴ 40

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 • 2.2k views

ADD COMMENT • link updated 3.3 years ago by Ram 43k • written 3.5 years ago by eridanus ▴ 40

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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 REPLY • link 3.5 years ago by LabCoatNomad ▴ 10

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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 REPLY • link 3.5 years ago by ATpoint 82k

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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 REPLY • link 3.5 years ago by eridanus ▴ 40

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

ADD REPLY • link 3.5 years ago by eridanus ▴ 40

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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 REPLY • link 3.5 years ago by eridanus ▴ 40

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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.