User: archana.bioinfo87
archana.bioinfo87 • 90
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Posts by archana.bioinfo87
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Comment:
C: what next after DEGs?
... Its all depend on your work objectives because you can do "n" number of analysis in research. ...
written 3 days ago by
archana.bioinfo87 • 90
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... Use standalone blast where you can make 1890 protein as a database (using makeblastdb) and rest 3 protein as a query. ...
written 4 days ago by
archana.bioinfo87 • 90
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... Dear, I think I already mentioned in my question that I have 9 different databases. Things which I already tried
1. I created 9 different databases using makeblastdb. And tried the loop for 1 database sequences blast with respect to other using loop. (~20 days ran but no result)
2. Tried the blast ...
written 4 days ago by
archana.bioinfo87 • 90
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... Sorry, may be I was unable to explain but I splited the query file not the DB. Already, I tried blastdb_aliastool but still waiting for result.
I am sorting the BLAST result to get the exact matched sequences only.
Thanks for your valuable suggestions. ...
written 5 days ago by
archana.bioinfo87 • 90
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... Thanks, yes i tested all databases before putting them in this big for loop. Till date only i can think the memory issue. Because for small seqeuences i am getting the results.
Thanks all for your suggestions ...
written 6 days ago by
archana.bioinfo87 • 90
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... Thanks, but already i tested with small sequence before putting them in loop. ...
written 6 days ago by
archana.bioinfo87 • 90
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... Yes, only one database will match with another 8 one by one. ...
written 6 days ago by
archana.bioinfo87 • 90
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... Thanks for your reply. As, I tried "*" in makeblastdb to make multiple databases at a time and it worked. Regarding complicated analysis... yes it is that is why I was trying to put in loop to get the result. As, it seems not working so I split the fasta file of all databases and added in loop. And ...
written 6 days ago by
archana.bioinfo87 • 90
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... I am trying to run this command on server
#!/bin/bash
# Sample Slurm Script for use with OpenMPI on Plato
# Begin Slurm directives with #SBATCH
#SBATCH --job-name=multidb_test2_$1
#SBATCH --nodes=10
#SBATCH --tasks-per-node=10
#SBATCH --cpus-per-task=1
#SBATCH --time ...
written 7 days ago by
archana.bioinfo87 • 90
• updated
7 days ago by
genomax ♦ 55k
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... Thanks but out file is empty and I think still its running. ...
written 9 days ago by
archana.bioinfo87 • 90
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