Hi I am using tximport to make a matrix of all TPM values, I have TSV files for many samples, which looks like:

Gene ID Gene Name Reference Strand Start End Coverage FPKM TPM ENSG00000187961.13 KLHL17 chr1 + 960587 965715 4,714223 2,219789 5,030543 ENSG00000187583.10 PLEKHN1 chr1 + 966497 975865 3,669177 2,59782 5,887248 ENSG00000187642.9 PERM1 chr1 - 975204 982093 1,092457 0,444985 1,008436

I have performed these commands:

all(file.exists(samples)) [1] TRUE tmp <- readtsv(samples[1]) Parsed with column specification: cols( Gene ID = colcharacter(), Gene Name = colcharacter(), Reference = colcharacter(), Strand = colcharacter(), Start = coldouble(), End = coldouble(), Coverage = coldouble(), FPKM = coldouble(), TPM = coldouble() ) tx2gene <- tmp[, c("Gene ID", "Gene Name")] txi <- tximport(samples, type = "kallisto", tx2gene = tx2gene, ignoreTxVersion = TRUE) Note: importing abundance.h5 is typically faster than abundance.tsv reading in files with read_tsv 1 Warning: 78724 parsing failures. row col expected actual file ... ......... .......... ......... ......................................................................... See problems(...) for more details.

Error in tximport(samples, type = "kallisto", tx2gene = tx2gene, ignoreTxVersion = TRUE) : all(c(abundanceCol, countsCol, lengthCol) %in% names(raw)) is not TRUE In addition: Warning message: Unnamed col_types should have the same length as col_names. Using smaller of the two.

After running this command, I have noticed that the TSV files have different row lengths i.e. some files contains 19682 genes, some contains 19684 genes,, so the number of rows are different in each file..

So I want to ask if there is a way to ignore this parameter or any other solution to this problem? Thanks

Those are not original abundance files, but have been modified. For example the effective lengths are missing, which are needed to run tximport.