Entering edit mode
10.1 years ago
Nai
▴
50
Respected Sir/ Madam,
I am Neha Goel from India. I am working on transcriptome sequence data from 454seq. I have 10Mbps data, I preprocessed (Quality filter/ Quality Trimming) and obtained the filtered file . For Denovo assembly I chase the velvet-Oases. I installed the velvet and it gave the contig.fa and Sequences.fa, Now I ran the command for Oases.
./oases 'directory name/' -merge yes -scaffolding yes -min_trans_lgth 200
But I get the transcripts.fa
with out any data (0 bytes).
I am not getting why is it so??? I ran the previous commands:
velveth dir 31 -fastq -short reads.fq
velvetg dir/ -read_trkg yes
I also have single read Roche data. Now Please guide me what should I do?
Doesn't 454 data mean that we use the
-long
(and not the-short
) flag forvelveth
?As the output contig.fa (13MB) and sequencs.fa (250MB)
when I am executing the command
(Here I gave velvet directory path) then it gives the following error:
When I set the path through command line as well as
.bashrc
but still its not working,Please guide me the steps what to do..
Could you maybe make sure you are pointing to where the actual
velveth
andvelvetg
binaries exist and not to the parent folder by mistake please? Sometimes the binaries are nested inside abin/
ordist/
folder and giving the parent folder does not work in these cases.I download velvet_1.2.10 in Downloads folder and untar it., make after that I set the categories and maxkmerlength through make command. After that I ran the command velveth then it was displaying
if I am running
This command executed..after that I ran
./velvetg
and continued with./oases
. It generated the transcript.faIf I am running
oases_pipeline_python
script its not executing.Now how can I find the number of transcripts, contigs and singletons from the contig.fa
There are a couple of ways you could solve this. While you're downloading, un-archiving and building velvet just fine, you still need to add the binaries to your PATH variable. Easiest way for you is to run
and then try running
oases_pipeline.py