Dear Bastien and All,
I really appreciate Mira. Thank you very much.
I have a question about the difference between singlets and NO_OVERLAP
sequences in debrislist file.
Singlets are important for my study. So I set sssip=yes and mrpc=1.
So I get “contigs” with single read. I really appreciate this function.
However, I also realised many sequences are in debrislist with NO_OVERLAP
annotated.
Those NO_OVERLAP sequences in debrislist file are long and looking very good
sequences.
How those sequences in debrislist file with NO_OVRELAP annotatation are
different from singlets?
I would very much appreciate you comment.
Best regards,
Lyu
I have attached my manifest file here.
project = 09
job = est,denovo,accurate
parameters = COMMON_SETTINGS
readgroup = SomePairedEndIlluminaReadsIGotFromTheLab
data = /R1.fastq /R2.fastq
technology = solexa
autopairing
segment_naming = solexa
parameters = -GE:not=7
parameters = -SK:not=7
parameters = -SK:pr=97
parameters = -SK:mmhr=10
parameters = -SK:bph=10
parameters = -HS:mnr=yes
parameters = -HS:nrr=10
parameters = -HS:ldn=no
parameters = -NW:cmrnl=no
parameters = -CO:mr=yes
parameters = -CL:ascdc=yes
parameters = SOLEXA_SETTINGS
parameters = -AL:mrs=97
parameters = -CO:mgqrt=35
parameters = -CO:mnq=40
parameters = -AS:mrpc=1
parameters = -AL:mo=35
parameters = -OUT:sssip=yes