After running multiple_join_paired_ends.py on my 600 Illumina MiSeq files, the output leaves each sample in individual folders. The folder has a unique name, but all of the files in each subdirectory have the name "fastqjoin.join.fastq."
In order to continue with split_libraries.py, I need to have all of the .fastq files in a single folder with unique names to identify the samples.
Is there a script to rename all of the files in each folder with the name of the folder they are in? This is how my filing system works...
/home/qiime/desktop/Final_Analysis/join_paired_ends_fastq-join/600 uniquely named folders, within each folder is a single joined .fastq file, but all of the files have the same name of "fastqjoin.join.fastq"
If each of those files could be renamed to the name of the folder they are in, I could just move them to another directory easily and each would have a unique identifier. Basically, I am trying to avoid individually going in and renaming each of the 600 files.
Any help would be greatly appreciated!
In order to continue with split_libraries.py, I need to have all of the .fastq files in a single folder with unique names to identify the samples.
Is there a script to rename all of the files in each folder with the name of the folder they are in? This is how my filing system works...
/home/qiime/desktop/Final_Analysis/join_paired_ends_fastq-join/600 uniquely named folders, within each folder is a single joined .fastq file, but all of the files have the same name of "fastqjoin.join.fastq"
If each of those files could be renamed to the name of the folder they are in, I could just move them to another directory easily and each would have a unique identifier. Basically, I am trying to avoid individually going in and renaming each of the 600 files.
Any help would be greatly appreciated!
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