Index of /examples/bioinformatics/oases/step_by_step

Name	Last modified	Size

Parent Directory		-
merged/	2019-09-09 19:03	-
oases_step_by_step.qsub	2019-09-09 19:03	601
out_21/	2019-09-09 19:03	-
out_23/	2019-09-09 19:03	-
test_reads.fa	2019-09-09 19:03	327K

Oases Example: step_by_step

Interactive Usage:


# load modules

scc4% module load velvet/1.2.10

scc4% module load oases/0.2.09






# print Oases command help:

scc4% oases






# print velveth command help:

scc4% velveth






# print velvetg command help:

scc4% velvetg






# Now run oases step by step, call velveth/velvetg and then oases one at a time:
Step 1: Run velveth on kmer ranger(multiple kmer, kmer_max<=31 and and kmer must be odd.  ), refer to Velvel manual: 

kmer=21,25,2 data=test_reads/fa, read length=75bp, output directory 'out'



scc4% velveth out 21,25,2 -short -fasta test_reads.fa






Step 2: Run velvetg for each kmer, one at a time to assemble each data: 
scc4% for k in $(seq 21 2 23) 
      do 
        velvetg  out_$k -read_trkg yes 
      done






Step 3: Run velvetg for each kmer, one at a time to assemble each data: 
scc4% for k in $(seq 21 2 23) 
      do 
        oases out_$k 
      done





Step 4: Run merge after obtain each kmer result: 

scc4% velveth merged 23 -long out*/transcripts.fa 

scc4% velvetg merged -read_trkg yes -conserveLong yes

scc4% oases merged -merge yes






>Batch Usage - Submit as a Job:

scc4% qsub -P my_project oases_step_by_step.qsub






Further Resources:
For more information on how to use the software, please view Oases manual:


https://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf




Contact Information:
Research Computing Services: help@scc.bu.edu





Note: Research Computing Services (RCS) example programs are provided
"as is" without any warranty of any kind. The user assumes the entire risk of
quality, performance, and repair of any defects.  You are encouraged to copy
and modify any of the given examples for your own use.