Thank you Maria. This is a big help for me. Taking your advice, here is what I did
veleth auto 25 -fastq -shortPaired1 myRef_shuffled.fq
velvetg auto_25 -exp_cov auto -ins_length1 150
I get
Final graph has 2 nodes and n50 of 1, max 1, total 2, using 0/10148414 reads
However, I get an empty contig.fa.
Now when when I try kmer 21,
velveth auto 21,25,3 -fastq -shortPaired1 myRef_shuffled.fq
velvetg auto_21 -exp_cov auto -ins_length1 150
I get some contigs, however, they do not align with my reference sequence (500 bases).
Do you see anything wrong I might be doing? I should get some contigs that align with the reference 100%.
veleth auto 25 -fastq -shortPaired1 myRef_shuffled.fq
velvetg auto_25 -exp_cov auto -ins_length1 150
I get
Final graph has 2 nodes and n50 of 1, max 1, total 2, using 0/10148414 reads
However, I get an empty contig.fa.
Now when when I try kmer 21,
velveth auto 21,25,3 -fastq -shortPaired1 myRef_shuffled.fq
velvetg auto_21 -exp_cov auto -ins_length1 150
I get some contigs, however, they do not align with my reference sequence (500 bases).
Do you see anything wrong I might be doing? I should get some contigs that align with the reference 100%.
Comment