Hi, I have performed RNA-seq data quantification with salmon v0.14.1. When I tried to import the results into DESeq2 with tximport I have got this error:

> txi <- tximport(quant_files, type="salmon", tx2gene = tx2gene, ignoreTxVersion = FALSE)
reading in files with read_tsv
1 2 Error: lexical error: invalid char in json text.
                                      /Users/pcanion/Desktop/CD24_M
                     (right here) ------^

Here is the code I used to get to that point:

if (file.exists("/Users/pcanion/Desktop/CD24_Maria/R/meta/tx2gene.csv")) {
    tx2gene <- read.delim("/Users/pcanion/Desktop/CD24_Maria/R/meta/tx2gene.csv", sep = ",")
} else {
ensembl = useEnsembl(biomart="ensembl", 
                     dataset="hsapiens_gene_ensembl",
                     host = 'www.ensembl.org',
                      mirror = "uswest")

t2g <- biomaRt::getBM(attributes = c('ensembl_gene_id',
                                     'ensembl_transcript_id',
                                     'external_gene_name'), 
                      mart = ensembl)
t2g <- dplyr::rename(t2g, 
                     trans_id = ensembl_transcript_id,
                     ens_gene = ensembl_gene_id, 
                     ext_gene = external_gene_name)

tx2gene <- dplyr::select(t2g, trans_id, ens_gene)

write.csv(tx2gene, file="/Users/pcanion/Desktop/CD24_Maria/R/meta/tx2gene.csv", row.names = FALSE, quote=FALSE)
}

# locate salmon outputs
quant_files <- list.files("/Users/pcanion/Desktop/CD24_Maria/Phoenix/outs", 
                          pattern="quant.sf", 
                          recursive = TRUE, full.names = TRUE)
dirs <- list.files("/Users/pcanion/Desktop/CD24_Maria/Phoenix/outs/")
names(quant_files) <- dirs
quant_files

# Load "transcript to gene"" file
tx2gene <- read.delim("/Users/pcanion/Desktop/CD24_Maria/R/meta/tx2gene.csv", sep = ",")

# tximport
txi <- tximport(quant_files, type="salmon", tx2gene = tx2gene, ignoreTxVersion = TRUE)

My list of quantification results looks like this:

> quant_files
                                                                    CD24_01_346-15-1_S1.salmon 
       "/Users/pcanion/Desktop/CD24_Maria/Phoenix/outs/CD24_01_346-15-1_S1.salmon/quant.sf" 
                                                                  CD24_02_402-6-1_sc_S2.salmon 
     "/Users/pcanion/Desktop/CD24_Maria/Phoenix/outs/CD24_02_402-6-1_sc_S2.salmon/quant.sf" 
                                                                  CD24_03_402-5-2_sc_S3.salmon 
     "/Users/pcanion/Desktop/CD24_Maria/Phoenix/outs/CD24_03_402-5-2_sc_S3.salmon/quant.sf" 
                                                                    CD24_04_346-15-5_S4.salmon 
       "/Users/pcanion/Desktop/CD24_Maria/Phoenix/outs/CD24_04_346-15-5_S4.salmon/quant.sf" 
                                                              CD24_05_402-5-2_Br_Met_S5.salmon 
 "/Users/pcanion/Desktop/CD24_Maria/Phoenix/outs/CD24_05_402-5-2_Br_Met_S5.salmon/quant.sf" 
                                                                 CD24_06_346-25-5_sc_S6.salmon 
    "/Users/pcanion/Desktop/CD24_Maria/Phoenix/outs/CD24_06_346-25-5_sc_S6.salmon/quant.sf" 
                                                                    CD24_07_346-15-4_S7.salmon 
       "/Users/pcanion/Desktop/CD24_Maria/Phoenix/outs/CD24_07_346-15-4_S7.salmon/quant.sf" 
                                                              CD24_08_402-6-1_Br_Met_S8.salmon 
 "/Users/pcanion/Desktop/CD24_Maria/Phoenix/outs/CD24_08_402-6-1_Br_Met_S8.salmon/quant.sf" 
                                                             CD24_09_346-25-5_Br_met_S9.salmon 
"/Users/pcanion/Desktop/CD24_Maria/Phoenix/outs/CD24_09_346-25-5_Br_met_S9.salmon/quant.sf" 

And the tx2gene dataframe looks like this:

> head(tx2gene,5)
         trans_id        ens_gene
1 ENST00000387314 ENSG00000210049
2 ENST00000389680 ENSG00000211459
3 ENST00000387342 ENSG00000210077
4 ENST00000387347 ENSG00000210082
5 ENST00000386347 ENSG00000209082

Would anyone be able to help me with this error? Thanks!

Can you see if this previous post helps fix the issue:

https://support.bioconductor.org/p/126276/