I have a total of 12 samples [6 infected sample (number- 7,8,9,10,11 and 12) of different time-point with their 6 control samples (number- 1,2,3,4,5 and 6)] from RNAseq, paired end (Illumina; GAIIx).
My Sample was distributed in 8 Lanes. Details:
LANE SAMPLE LANE_1: 7,8,9,10 [Control samples] LANE_2: 1,2,3,4,5,6 [Infected samples] LANE_3: 11,12,7,8 [Control samples] LANE_4: PhiX control lane LANE_5: 9,10,11,12 [Control samples] LANE_6: 1,2,3,4 [Infected samples] LANE_7: 5,6,1,2 [Infected samples] LANE_8: 3,4,5,6 [Infected samples]
The data provided to me was in bcl format, which i have converted them into fastq format using bcltofastq software. Now, I have 16 fastq files, both forward and reverse:
Right Reads Left Reads LANE_1_R2.fq LANE_1_R1.fq LANE_2_R2.fq LANE_2_R1.fq LANE_3_R2.fq LANE_3_R1.fq LANE_4_R2.fq LANE_4_R1.fq LANE_5_R2.fq LANE_5_R1.fq LANE_6_R2.fq LANE_6_R1.fq LANE_7_R2.fq LANE_7_R1.fq LANE_8_R2.fq LANE_8_R1.fq
For the denovo assembly do i need to feed all the R1 reads as left and R2 reads as right in TRINITY and do I need to remove PhiX Lane.
How to align reads from each sample to the reference because i dont have seperate fastq file of each sample.
Many thanks in advance!