Hi
I'm trying to run Velvet on SOLiD data. Have done as follows:
Compiled Velvet with color-space support, and increased hash size support.
Creates a data set as follow:
And then run velvetg_de as follow:
This gives 0 contigs in contigs.fa. Started to check other hash sizes 21, 31 and 41. All resulting in 0 contigs. I know that this data should have some contigs as ~45 % was successfully aligned with MosaikAligner.
I noticed that all sequences in file "Sample20_hash41/Sequences" has the exact same sequence "TAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA". Is this normal?
Did I miss some crucial step?
Best
/Magnus
I'm trying to run Velvet on SOLiD data. Have done as follows:
Compiled Velvet with color-space support, and increased hash size support.
Code:
make 'MAXKMERLENGTH = 50' & color
Code:
velveth_de Sample20_hash41 41 -short Sample20.csfasta
Code:
velvetg_de Sample20_hash41
I noticed that all sequences in file "Sample20_hash41/Sequences" has the exact same sequence "TAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA". Is this normal?
Did I miss some crucial step?
Best
/Magnus
Comment