Hi,
I am trying to generate EST assembly from .scf file. The expected assembly
size is ~500nt. Since I don't have idea about technology used and insert
length, I am facing problem. Is there any way with which we can generate
assembly when don't have technology information and insert length.
Following is the way I tried to generate assembly: 1) Converting scf file
to fasta and writing in manifest file: job = est parameters = --noqualities
-GE:not=4 -NW:cnfs=warn,cdrn=warn readgroup =
DataIlluminaForPairedEnd500bpLib data =
/home/mandar/MLST/trace_files/IN_1-31_F.fasta
/home/mandar/MLST/trace_files/IN_1-31_R.fasta technology = solexa strain =
bchoc_se1 template_size = 250 750 segment_placement = ---> <--- With this I
am encountering error: Fatal error (may be due to problems of the input
data or parameters):
********************************************************************************
* MIRA found readgroups where pairs are expected but no read has a partner.
* * See log above and then check your input please (either manifest file or
data * * files loaded or segment_naming scheme). *
********************************************************************************
->Thrown: void Assembly::basicReadGroupChecks() ->Caught: main Please help
me to generate good assembly starting with .scf file.
Regards,
Mandar
