User: Fatima
Fatima • 860
- Reputation:
- 860
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- United states
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- fsharifi4
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Posts by Fatima
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... I clicked on the link you posted, clicked on the tab for `Refseq Genome`, clicked on the assembly:
https://www.ncbi.nlm.nih.gov/assembly/GCF_009858895.2
Then clicked on `FTP directory for GenBank assembly`
You can get the fasta sequence by clicking on
https://ftp.ncbi.nlm.nih.gov/genomes/all/GC ...
written 1 day ago by
Fatima • 860
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... You can get the assembly ids, and download from the ftp, for example:
https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/009/858/895/GCA_009858895.3_ASM985889v3/ ...
written 1 day ago by
Fatima • 860
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... Could you try `ls human_genome*` while you're in `/my/path/human_genome_DB` and tell us what you have in that directory?
I assume `/my/path/human_genome_DB` is a directory so it won't work for `-db`. ...
written 2 days ago by
Fatima • 860
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Comment:
C: HMMER software error message
... Yes, but OP was using both for one file. ...
written 2 days ago by
Fatima • 860
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Comment:
C: HMMER software error message
... Can you try without `--cut_ga` and see if it works?
Also please make sure `HMMER_R` is not a folder. For `--tblout` you need to specify a file name, so if `HMMER_R` is a folder that path won't work. ...
written 3 days ago by
Fatima • 860
1
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Answer:
C: HMMER software error message
... `-o` is redundant as you are using `--tblout`
This should work:
hmmscan --cut_ga --tblout /cluster/work/users/ahmedbar/191129_M01132.Project_Petersen-DNAlibs2-2019-11-06/HMMER_R /cluster/work/users/ahmedbar/Resfams-full.hmm /cluster/work/users/ahmedbar/191129_M01132.Project_Petersen-DNAl ...
written 3 days ago by
Fatima • 860
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... Do any of these links seem helpful?
https://metacyc.org/META/NEW-IMAGE?type=PATHWAY&object=P101-PWY&ENZORG=ALL
https://www.brenda-enzymes.org/enzyme.php?ecno=1.2.1.11 ...
written 4 days ago by
Fatima • 860
0
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... The screenshot is not visible. ...
written 10 days ago by
Fatima • 860
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... Hi! You can try `Fun4me`. Since you already have the assembled contigs, you can input them using option `-r 0`.
https://sourceforge.net/p/fun4me/code/ci/master/tree/
It annotates the genes, and provides GO information, EC numbers, Pathway informations from metaCyc, plus outputs a table with functi ...
written 11 days ago by
Fatima • 860
0
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1
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119
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... Yes, -gff3 probably calls a different set of functions. ...
written 12 days ago by
Fatima • 860
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For A: bash script for RNA seq analysis
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