Hi I want to open an fastq file with readFastq() but it gives me an error :

is the invalid character a space in the file, if it is how I can remove it?

> f<- readFastq("a.fastq")
Error: Input/Output
  file(s):
    a.fastq
  message: invalid character '



> sessionInfo( )
R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] ShortRead_1.46.0            GenomicAlignments_1.24.0    SummarizedExperiment_1.18.2 DelayedArray_0.14.1         matrixStats_0.58.0         
 [6] Biobase_2.48.0              Rsamtools_2.4.0             GenomicRanges_1.40.0        GenomeInfoDb_1.24.2         Biostrings_2.56.0          
[11] XVector_0.28.0              IRanges_2.22.2              S4Vectors_0.26.1            BiocParallel_1.22.0         BiocGenerics_0.34.0        

loaded via a namespace (and not attached):
 [1] rstudioapi_0.13        zlibbioc_1.34.0        lattice_0.20-41        jpeg_0.1-8.1           hwriter_1.3.2          tools_4.0.3           
 [7] grid_4.0.3             png_0.1-7              latticeExtra_0.6-29    crayon_1.4.1           Matrix_1.3-2           GenomeInfoDbData_1.2.3
[13] RColorBrewer_1.1-2     bitops_1.0-6           RCurl_1.98-1.2         compiler_4.0.3

Probably the simplest thing you can do is to cut the file in half, and see if you can isolate where the error is. Or, if an 8 line fastq won't import, you have a pervasive problem.

If you have 'U' in your FASTQ files I think that will be a problem. I can barely understand C code, but in read_solexa_fastq it says

SEXP read_solexa_fastq(SEXP files, SEXP withId)
{
    int i, nfiles, nrec = 0;
    const char *fname;
    SEXP ans = R_NilValue, nms = R_NilValue;

    if (!IS_CHARACTER(files))
        Rf_error("'%s' must be '%s'", "files", "character");
    if (!IS_LOGICAL(withId) || LENGTH(withId) != 1)
        Rf_error("'%s' must be '%s'", "withId", "logical(1)");

    nfiles = LENGTH(files);
    nrec = (int) _count_lines_sum(files) / LINES_PER_FASTQ_REC;
    PROTECT(ans = NEW_LIST(3));
    SET_VECTOR_ELT(ans, 0, _NEW_XSNAP(nrec, "DNAString"));      /* sread */

And if it's saying the input data have to be of class DNAString then obviously a 'U' is a non-starter. The help page for readFastq says it uses the IUPAC alphabet from Biostrings, and in that package we have

> DNA_ALPHABET
 [1] "A" "C" "G" "T" "M" "R" "W" "S" "Y" "K" "V" "H" "D" "B" "N" "-" "+" "."

So again, I think a 'U' in your FASTQ file will be problematic because it's not a DNA letter.