User: Fatima

gravatar for Fatima
Fatima860
Reputation:
860
Status:
Trusted
Location:
United states
Twitter:
fsharifi4
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Google Scholar Page
Last seen:
an hour ago
Joined:
4 years ago
Email:
f************@gmail.com

Posts by Fatima

<prev • 267 results • page 1 of 27 • next >
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Comment: C: how to batch download SARS-CoV-2 sequences data from NCBI?
... 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 Fatima860
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Comment: C: how to batch download SARS-CoV-2 sequences data from NCBI?
... 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 Fatima860
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Comment: C: BLAST Database error: No alias or index file found for nucleotide database
... 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 Fatima860
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Comment: C: HMMER software error message
... Yes, but OP was using both for one file. ...
written 2 days ago by Fatima860
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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 Fatima860
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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 Fatima860
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Comment: C: Obtaining directionality of pathways
... 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 Fatima860
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Comment: C: Problem loading data from metadata file on Cytoscape
... The screenshot is not visible. ...
written 10 days ago by Fatima860
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Comment: C: Metagenomics - Functional analysis
... 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 Fatima860
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Comment: C: Error with gff file while building snpeff database
... Yes, -gff3 probably calls a different set of functions. ...
written 12 days ago by Fatima860

Latest awards to Fatima

Voter 26 days ago, voted more than 100 times.
Autobiographer 5 weeks ago, has more than 80 characters in the information field of the user's profile.
Scholar 6 weeks ago, created an answer that has been accepted. For A: bash script for RNA seq analysis
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: bash script for RNA seq analysis
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Samtools depth input
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Samtools depth input
Scholar 8 months ago, created an answer that has been accepted. For A: bash script for RNA seq analysis
Centurion 9 months ago, created 100 posts.
Scholar 10 months ago, created an answer that has been accepted. For A: bash script for RNA seq analysis
Scholar 10 months ago, created an answer that has been accepted. For A: bash script for RNA seq analysis
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Parsing gff files using python and awk
Popular Question 2.7 years ago, created a question with more than 1,000 views. For concatenating different columns of different files bash script
Scholar 3.2 years ago, created an answer that has been accepted. For A: bash script for RNA seq analysis
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: bash script for RNA seq analysis
Supporter 3.2 years ago, voted at least 25 times.

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