I am a little bit confused analyzing my RNASeq data. However, I sent 12 samples to the sequencing facility, 6 control samples and 6 knockdown samples. However I only got 3 files back from the sequencing facilty:
lane1_R1.fastq.gz lane1_R2.fastq.gz lane1_R3.fastq.gz
Why do I get 3 files back, when I sent 12 samples to the facility? Thats really confusing... Do I maybe need to demultiplex my data? I tried to analyze the data without demultiplexing with the following workflow on GALAXY so far:
FATSQC -> Trimmomatic -> HISAT2 -> StringTie -> SeSeq2 -> ...
However StringTie to read the quantification does not work really.. How can I solve this?
The descrption of RNASeq data I got from the seqcuencing facility says:
"1,2,3,4,5,6,7,8,9,10,11,12 single + index nn RNAseq Y50N,Y8,Y8 1 1 Galaxy no_demux "
However, I am really confused and would be glad for any help from you guys!