Question: Rsubread - Alignment-Error in normalizePath
0
gravatar for devarts
6 months ago by
devarts20
devarts20 wrote:

Hi All. I'm trying to an alignment for multiple files, paired end, using Rsubread. I set up the readfile vector with file names as follows.

read1 <- list.files(path= "path to/Yarrowia_lipolytica/Genewiz-us-ngs-00_fastq", pattern = "*_R1_001.fastq.gz$")
read2 <- list.files(path= "path to/Genewiz-us-ngs-00_fastq", pattern = "*_R2_001.fastq.gz$")

That seems to work, in example reads1 appears to be chr [1:24] "F353-B-gku_R1_oo1.fasta.gz"....

But, when I try to run align, as follows, I get an error that is a mystery to me.

align(index = "index", readfile1 = reads1, readfile2 = reads2, output_file = "./Rsubread_alignment.BAM", input_format = "FASTQ", output_format = "BAM")

Error in normalizePath(files, mustWork=mustWork)
: path[1] = "F353-B-gku_R1_oo1.fasta.gz".: No such file or directory

I wonder if the file names need the whole path attached somehow?

Any help would be much appreciated.

Thanks, David

rna-seq rsubread alignment • 204 views
ADD COMMENTlink modified 6 months ago • written 6 months ago by devarts20

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.
code_formatting

ADD REPLYlink written 6 months ago by Ram32k

Thank You. I'm new.

ADD REPLYlink written 6 months ago by devarts20

Thank You. That worked.

ADD REPLYlink written 6 months ago by devarts20

Please only add answers when you're answering the question on the top-level post. This psot should have been a comment on my answer. I've moved it to a comment on the top-level post for now.

Please accept my answer (the green check mark on the left) so the post is marked as solved.

ADD REPLYlink written 6 months ago by Ram32k

Whoops. My bad. I am learning.

ADD REPLYlink written 6 months ago by devarts20

That's OK. Welcome to biostars!

ADD REPLYlink written 6 months ago by Ram32k
3
gravatar for Ram
6 months ago by
Ram32k
Baylor College of Medicine, Houston, TX
Ram32k wrote:

I wonder if the file names need the whole path attached somehow?

Yes. Add full.names = TRUE to list.files() and you should be all set.

ADD COMMENTlink written 6 months ago by Ram32k

Thank You. Yes. That worked well. :)

ADD REPLYlink written 6 months ago by devarts20
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