What is readsize?

[yangyxt]

Dear Firtina,

THanks for the update. I still have some confusion about the definition of the input argument READSIZE.

Is this metric reflecting the number of pairs of reads in my prepared fastq file? or the total number of reads (e.g. 2 times number of pairs, in my case I don't have singleton reads, every read is paired. ) or the read length?

In extract reads.sh, you typed:

Can I ask why comparing the PNEXT in SAM with readsize? array[8] is supposed to be the 8th field delimited by tab in a line of SAM format, which is PNEXT instead of CIGAR string.

From this command, I suppose readsize is read length. While not every read has the exact same length. So could you pls help explain a bit of this argument's usage? Much appreciated.