I am simulating test reads with
randomreads.sh from BBMap package.
My command is
/Software/bbmap/randomreads.sh ref=C_glabrata_CBS138_current_chromosomes.fasta out1=read1.fastq out2=read2.fastq build=1 length=10 reads=2 coverage=-1 replacenoref=t simplenames=t seed=-1 paired=t metagenome=t addpairnum=t
The output is:
@0_+106297_106306_ChrM_C_glabrata_CBS138 (1402899 nucleotides) 1: AGGTTTTAAT + 989945?446 @1-_438159_438168_ChrJ_C_glabrata_CBS138 (1195129 nucleotides) 1: ATATCTTCCT + AA?CB?@bcb`
for read2 :
@0_-761178_761187_ChrM_C_glabrata_CBS138 (1402899 nucleotides) 2: AGCAGAGAGA + ?>64844:64 @1+_646646_646655_ChrJ_C_glabrata_CBS138 (1195129 nucleotides) 2: TGCCAGTTTC + ??B@A?><@>
As far as I understand the reads @0 from read1 and @0 from read2 correspond to the read pair. However based on their coordinates they are super far away form each other. Is this a normal behaviour of the software?
P.S. Hope Brian Bushnell will see this post :)