I have a kalliso-created abundance.h5 file but the filename (ES_1_high_28881_CGATGT_abundance.h5) includes information about the sample. When I try to import this file using tximport v1.10.0 I get an error. tximport thinks that the file is a .tsv file.
However, if I create a symlink named abundance.h5, I can load that perfectly well.
Is there a way to tell tximport that the file really is a kallisto h5 file?
data <- tximport( 'ES_1_high_28881_CGATGT_abundance.h5' , type = "kallisto" , tx2gene=tx2gene , ignoreAfterBar=TRUE )
Note: importing `abundance.h5` is typically faster than `abundance.tsv`
reading in files with read_tsv
1 Error in read_tokens_(data, tokenizer, col_specs, col_names, locale_, :
embedded nul in string: '\0\xfbLΦ(\x98Hr1'
In addition: Warning message:
Unnamed `col_types` should have the same length as `col_names`. Using smaller of the two.
> system('ln -s ES_1_high_28881_CGATGT_abundance.h5 abundance.h5')
> data <- tximport( 'abundance.h5' , type = "kallisto", tx2gene=tx2gene , ignoreAfterBar=TRUE ) 1 summarizing abundance summarizing counts summarizing length summarizing inferential replicates