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
can I use readFastq() to read RNA fastq file? because when I remove the letter U from the file issue is resolved.