STAR for single vs paired reads

[splaisan]

--readFilesIn parameter:

# for single end: 
    --readFilesIn Reads.fastq

# for paired-end 
    --readFilesIn Read1.fastq Read2.fastq

# for multiple fastq(.gz) in a single run (several lanes of the same library for instance)
    --readFilesIn Read1a.gz,Read1b.gz Read2a.gz,Read2b.gz

# If the reads are all zipped, add this to the command
    --readFilesCommand zcat