Dear all,
I have one illumina TruSeq long read assembly and three MiSeq 2x75 short reads assemblies. I want to merge the long read assembly to each of the short reads assemblies so that at the end I will have three total assmblies:
1) Long read scaffold + Velvet scaffolds
2) Long read scaffold + AbySS scaffolds
3) Long read scaffold + SOAP scaffolds
However, I do not know how to denife the parameters in the config file, it looks like this:
[global]
mateAn_A=???
mateAn_B=???
bowtie2_read1=TSSLR-BDA11_LongRead.fastq
bowtie2_read2=oenopla-reads1.fastq
bowtie2_maxins=???
bowtie2_minins=???
bowtie2_threads=1
meta2fasta_keepUnaligned=0
meta2fasta_sizeUnaligned=??? ???
nucmer_l=50
nucmer_c=300
nucmer=/home/ktsang/.conda/envs/MyVirtualEnv/bin/nucmer
delta-filter=/home/ktsang/.conda/envs/MyVirtualEnv/bin/delta-filter
show-coords=/home/ktsang/.conda/envs/MyVirtualEnv/bin/show-coords
bowtie2=/home/ktsang/.conda/envs/MyVirtualEnv/bin/bowtie2
bowtie2-build=/home/ktsang/.conda/envs/MyVirtualEnv/bin/bowtie2-build
samtools=/home/ktsang/.conda/envs/MyVirtualEnv/bin/samtools
[1]
fasta=oenopla_VOscaffolds011216.fasta
ID=LongRead
[2]
fasta=scaffolds/SOAPdenovo.final.scaffolds.fasta
ID=SOAP
I have read the manual but I still do not understand. What number I should put at mateAn_A, mateAn_B, bowtie2_maxins, bowtie2_minins, meta2fasta?
I do not know the insert size of the short reads, can someone help/advise me with deciding he numbers in bold?
Thank you!
Kenny
