I have several samples each in their own folder. Paired end. Each sample's folder looks something like this in the following format:
****_L006_R1_001.fastq.gz and ******_L006_R2_001.fastq.gz
****_L006_R1_002.fastq.gz and ******_L006_R2_002.fastq.gz.
...
.
.
.
****_L006_R1_006.fastq.gz and ******_L006_R2_006.fastq.gz.
****_L007_R1_001.fastq.gz and ******_L007_R2_001.fastq.gz.
.
.
.
****_L007_R1_006.fastq.gz and ******_L007_R2_006.fastq.gz.
What I've done so far is merged all the R1s (irrespective of lanes), and all R2s (again, irrespective of lanes). And have been aligning them, and calling fusions on the merged R1.
How do I interpret any fusion results of ****_L006_R1_002.fastq.gz and ******_L006_R2_002.fastq.gz. VERSUS R1-merged.fastq.gz vs R2-merged.fastq.gz? Does R1-merged/R2-merged represent the entire sample properly or should I call fusion on each R1,R2 and find some sort of average?
This also applies to finding indels/cnvs/etc, do you guys usually call it on the merged fastq file or each unmerged one, and then find an average?
thank you!
****_L006_R1_001.fastq.gz and ******_L006_R2_001.fastq.gz
****_L006_R1_002.fastq.gz and ******_L006_R2_002.fastq.gz.
...
.
.
.
****_L006_R1_006.fastq.gz and ******_L006_R2_006.fastq.gz.
****_L007_R1_001.fastq.gz and ******_L007_R2_001.fastq.gz.
.
.
.
****_L007_R1_006.fastq.gz and ******_L007_R2_006.fastq.gz.
What I've done so far is merged all the R1s (irrespective of lanes), and all R2s (again, irrespective of lanes). And have been aligning them, and calling fusions on the merged R1.
How do I interpret any fusion results of ****_L006_R1_002.fastq.gz and ******_L006_R2_002.fastq.gz. VERSUS R1-merged.fastq.gz vs R2-merged.fastq.gz? Does R1-merged/R2-merged represent the entire sample properly or should I call fusion on each R1,R2 and find some sort of average?
This also applies to finding indels/cnvs/etc, do you guys usually call it on the merged fastq file or each unmerged one, and then find an average?
thank you!
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