I have RNA-seq from two sequencing batches; Lab technician says that he has run the RNA expression quantification two times in bathes 1 and 2 for example
tumor 1 in batch 1 and tumor 1 in batch 2 , normal 2 in batch1 and normal 2 in batch 2. This is my design for DESeq2
> head(mycols) condition batch N_1_305 N 1 N_1_310 N 1 N_1_337 N 1 N_1_353 N 1 T_1_305 T 1 T_1_310 T 1 > tail(mycols) condition batch T_2_337 T 2 T_2_338 T 2 T_2_344 T 2 T_2_346 T 2 T_2_349 T 2 T_2_353 T 2 >
I got this PCA plot
In PCA plot I am seeing for instance
T_1_337 (batch1) has been placed too close to T_2_337 (batch2)
Then I used svd for detecting hidden batch
Does this mean that there is no big batch effect between experimental runs and I can concatenate the fastqs from both batches for each sample (technical replication) or collapse technical replicates afterwards?
Please help me to interpret these Thank you
Sorry @Devon, I have 4 lanes for each samples (paired end) in each of experimental runs; For concatenating fastq files can I do like this ?
cat fastq1_lane1_batch1 fastq1_lane1_batch2 fastq1_lane2_batch1 fastq1_lane2_batch2 fastq1_lane3_batch1 fastq1_lane3_batch2 fastq1_lane4_batch1 fastq1_lane4_batch2 > fastq1 cat fastq2_lane1_batch1 fastq2_lane1_batch2 fastq2_lane2_batch1 fastq2_lane2_batch2 fastq2_lane3_batch1 fastq2_lane3_batch2 fastq2_lane4_batch1 fastq2_lane4_batch2 > fastq2