Bowtie2 no build the index
Hello, this is my first time using R to create an index with bowtie2. I'm using R on windows, I've installed Rbowtie2 and Rsamtools with "BiocManager::install()". But when I'm trying to index the genome "Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa" in the folder "Chromosomes" I'm getting this:
Can you help me or give me some advice? Thank you.
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Carlo Yague
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Corona Cano •
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Did you read the manual to see exactly how the command bowtie2_build should be used?
Yes, I even tried the following example and got the same thing
do you have access to a cluster, or a linux box? an example command would be:
it is so easy, you dont need R to run it
Moving this to a comment since it is not answering the question in the original post.
What is the issue exactly ? To have the function returns
NULLis not an a problem on its own. Have you looked in the folderChromosomes/if the bowtie2 index is built ? The files should be namedyeast.x.bt2oryeast.x.bt2l(where x is an integer).I've searched the folder but the index is not built, only the fasta file is there.
Ok, have you tried to add the option
--verboseoption instead of--quietand see if you can get more details about what went wrong ?Can you explain me how to do it? Thanks
I don't know how to explain other than that: replace the option (= the text you write in the console when writing the
bowtie2_buildcommand) "--quiet" by "--verbose".I've tried, but I've got the same.
Do you have python installed ? On Windows, it is said that you need both perl and python installed to make bowtie2-build work: