I have all file names for each paired-end fastq pair as shown below. Could you please suggest how I can extract all fastq.gz files in a single folder?
sample name:
188833984]$ ls
Leaf_T1_FD_R10_L001-ds.3b884c360b1e4ae185408a613b90a3bc
Leaf_T1_FD_R2_L001-ds.7db8eb7e3426486db549426601b3a0bd
Leaf_T1_FD_R3_L001-ds.147177ecc03a46ccbbce3162d1185a0a
pair end file within sample name Leaf_T1_FD_R10_L001-ds.3b884c360b1e4ae185408a613b90a3bc
188833984]$ cd Leaf_T1_FD_R10_L001-ds.3b884c360b1e4ae185408a613b90a3bc
Leaf_T1_FD_R10_L001-ds.3b884c360b1e4ae185408a613b90a3bc]$ ls
Leaf-T1-FD-R10_S73_L001_R1_001.fastq.gz
Leaf-T1-FD-R10_S73_L001_R2_001.fastq.gz
I need all in fastq.gz format but the problem is that each sample, pair end R1 and R2 fastq reads in a single folder like this: and I need to extract all samples files in a single folder
fastq.gz
tofastq
)? What is the final outcome you are expecting from the example you give? $\endgroup$fastq.gz
files found in various subdirectories tofastq
files in a single location. OP should probably decompress them where they are and create soft-links to them in their directory of choice. $\endgroup$Leaf_T1_FD_R10_L001-ds.3b884c360b1e4ae185408a613b90a3bc
with two files, anR1
and anR2
, so what is the problem? The files seem to already be in separate directories. Can you please edit and show us what the final result you want is? $\endgroup$