No more special reasons，if I want treat pair-end files (so one sample two xxx.fastq.gz files) as single-end to process.
- It means double sequence coverage?
- For the align step by star, should I merge these two files together
to map and I wonder how to merge just by
cat samplex_R1.fastq.gz samplex_R2.fastq.gz, or give up one file of them two? Orjust do map firstly as single-end(I worried about this way, after all, the contains of file are different), then merge their bam files together?
- I confused about why wc -l
samplex_R1.fastq.gzis different from
wc -l samplex_R2.fastq.gzsince they are pair?
Any idea will be very grateful!!!