Biological replicates?
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johnsolk commented
It looks like there are only 2 biological samples in these files, is that correct? Each set of R1/R2 files (001, 002, 003, 004, 005) appear to have the same barcode. For DE analysis, is it better to have all of the biological replicates from this experiment?
(pondenv)ubuntu@ip-172-31-30-249:/mnt/work/data$ ls -lah
total 120M
drwxrwxr-x 3 ubuntu ubuntu 4.0K Dec 22 22:43 .
drwxrwxr-x 8 ubuntu ubuntu 4.0K Dec 22 23:12 ..
-r--r--r-- 1 ubuntu ubuntu 7.6M Dec 14 2013 0Hour_ATCACG_L002_R1_001.extract.fastq.gz
-r--r--r-- 1 ubuntu ubuntu 7.7M Dec 14 2013 0Hour_ATCACG_L002_R1_002.extract.fastq.gz
-r--r--r-- 1 ubuntu ubuntu 7.6M Dec 14 2013 0Hour_ATCACG_L002_R1_003.extract.fastq.gz
-r--r--r-- 1 ubuntu ubuntu 7.6M Dec 14 2013 0Hour_ATCACG_L002_R1_004.extract.fastq.gz
-r--r--r-- 1 ubuntu ubuntu 2.8M Dec 14 2013 0Hour_ATCACG_L002_R1_005.extract.fastq.gz
-r--r--r-- 1 ubuntu ubuntu 8.0M Dec 14 2013 0Hour_ATCACG_L002_R2_001.extract.fastq.gz
-r--r--r-- 1 ubuntu ubuntu 8.1M Dec 14 2013 0Hour_ATCACG_L002_R2_002.extract.fastq.gz
-r--r--r-- 1 ubuntu ubuntu 8.1M Dec 14 2013 0Hour_ATCACG_L002_R2_003.extract.fastq.gz
-r--r--r-- 1 ubuntu ubuntu 8.0M Dec 14 2013 0Hour_ATCACG_L002_R2_004.extract.fastq.gz
-r--r--r-- 1 ubuntu ubuntu 2.9M Dec 14 2013 0Hour_ATCACG_L002_R2_005.extract.fastq.gz
-r--r--r-- 1 ubuntu ubuntu 5.2M Dec 14 2013 6Hour_CGATGT_L002_R1_001.extract.fastq.gz
-r--r--r-- 1 ubuntu ubuntu 5.2M Dec 14 2013 6Hour_CGATGT_L002_R1_002.extract.fastq.gz
-r--r--r-- 1 ubuntu ubuntu 5.2M Dec 14 2013 6Hour_CGATGT_L002_R1_003.extract.fastq.gz
-r--r--r-- 1 ubuntu ubuntu 5.2M Dec 14 2013 6Hour_CGATGT_L002_R1_004.extract.fastq.gz
-r--r--r-- 1 ubuntu ubuntu 4.9M Dec 14 2013 6Hour_CGATGT_L002_R1_005.extract.fastq.gz
-r--r--r-- 1 ubuntu ubuntu 5.4M Dec 14 2013 6Hour_CGATGT_L002_R2_001.extract.fastq.gz
-r--r--r-- 1 ubuntu ubuntu 5.4M Dec 14 2013 6Hour_CGATGT_L002_R2_002.extract.fastq.gz
-r--r--r-- 1 ubuntu ubuntu 5.4M Dec 14 2013 6Hour_CGATGT_L002_R2_003.extract.fastq.gz
-r--r--r-- 1 ubuntu ubuntu 5.5M Dec 14 2013 6Hour_CGATGT_L002_R2_004.extract.fastq.gz
-r--r--r-- 1 ubuntu ubuntu 5.1M Dec 14 2013 6Hour_CGATGT_L002_R2_005.extract.fastq.gz
drwxrwxr-x 2 ubuntu ubuntu 4.0K Dec 22 22:44 extract