"align" in rsubread only reading 1 out of 6 of my input files

Question

[nikalix]

Hi all,

I'm trying to align 6 rnaseq fastq.gz files to the index i just build using rsubread, but every time I run the command

align(index="zfish_index", readfile1= readfile1, readfile2=NULL, type= "rna", input_format="gzFASTQ",output_format="BAM")  

(readfile1 is the name of the 6 input files; ive checked that it actually contains all 6)

the program runs but in the console it says that the input file is only the first file listed in readfile1. Is there something I'm obviously doing wrong or is this how it normally runs? I hope that makes sense I'm a complete r novice and any advice is appreciated.

Thanks!!

Answer 1

[Gordon Smyth]

If readfile is a character vector of six file names, then align will align all of them, but it will do so one at a a time. Until the first file is finished, the console will only mention the first file. Then the console will show the second file. And so on.

If you need more help, you would need to show the contents of readfile1, for example by print(readfile1).