dear all,
I was trying to use contigs that are assembled by another program for scaffolding using SOAPdenovo.
I was looking at the example, given by soap writers, how to make your config file. However, I could not figure out how to put the inputs. It is very clear how I should add the short matepairs.
e.g.
q1=/path/**LIBNAMEB**/fastq_read_1.fq
q2=/path/**LIBNAMEB**/fastq_read_2.fq
q=/path/**LIBNAMEB**/fastq_read_single.fq
f=/path/**LIBNAMEB**/fasta_read_single.fa
how can I include the long contgs file from another de novo assembly, some around 40kb, in this .config file for scaffolding using mate pairs.
Thank you very much,
cheers,
Ashu
I was trying to use contigs that are assembled by another program for scaffolding using SOAPdenovo.
I was looking at the example, given by soap writers, how to make your config file. However, I could not figure out how to put the inputs. It is very clear how I should add the short matepairs.
e.g.
q1=/path/**LIBNAMEB**/fastq_read_1.fq
q2=/path/**LIBNAMEB**/fastq_read_2.fq
q=/path/**LIBNAMEB**/fastq_read_single.fq
f=/path/**LIBNAMEB**/fasta_read_single.fa
how can I include the long contgs file from another de novo assembly, some around 40kb, in this .config file for scaffolding using mate pairs.
Thank you very much,
cheers,
Ashu