Rsubread - Alignment-Error in normalizePath
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22 months ago
devarts ▴ 40

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 • 876 views
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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

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Thank You. I'm new.

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Thank You. That worked.

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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.

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Whoops. My bad. I am learning.

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That's OK. Welcome to biostars!

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22 months ago
Ram 36k

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.

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Thank You. Yes. That worked well. :)

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