User: Fatima

gravatar for Fatima
Fatima610
Reputation:
610
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Trusted
Location:
United states
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fsharifi4
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Google Scholar Page
Last seen:
1 day, 8 hours ago
Joined:
3 years, 10 months ago
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Posts by Fatima

<prev • 196 results • page 1 of 20 • next >
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Answer: A: Convert Loci to Gene Names?
... I'm not familiar with plant databases, but do you have their sequences? Have you tried blastx? Have you tried to see which databases have the information that you're looking for? http://planttfdb.gao-lab.org/tf.php?sp=Mtr&did=Medtr3g093830.1 https://phytozome-next.jgi.doe.gov/report/gene/Dca ...
written 8 days ago by Fatima610
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Comment: C: Hypothetical protein in Prokka
... You can use blastp to find similar proteins. Search for the conserved motifs in the protein using (cdd/pfam). Use GO information, pathways,..... depending on what you're looking for. ...
written 10 days ago by Fatima610
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Answer: A: Variant Call Format (.vcf) conversion to .bam
... https://www.biostars.org/p/160229/ ...
written 12 days ago by Fatima610
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Answer: A: Bedtools intersect not reporting all overlaps
... I'm not sure, but I think it's because f is 0.9, which restricts the output to when they have at least 90% overlap, in your example I think they only have 10% overlap. What's -wao? Have you tried -wb or -wa -wb? ...
written 3 months ago by Fatima610
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Comment: C: Error Muscle alignment (msa package, through Rscript)
... **Are your sequence headers unique? Are you using a profile? Could you provide the command that you're using?** This is the part of the code that gives you the error: void MSA::SetIdCount(unsigned uIdCount) { if (m_uIdCount > 0) { if (uIdCount & ...
written 4 months ago by Fatima610
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Comment: C: Extract fasta sequences based on ids file
... Are you sure? Because when I changed it to $1 and tried your sample data, I got correct results, but when it was $0 I got extra sequences as you mentioned. If you'd like to use my command line, you need single line sequences. You can use the command line in this link to convert your multi-line se ...
written 4 months ago by Fatima610
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Comment: C: Extract fasta sequence from multifasta file using id and position in range
... `; done` was missing from two of my commands. I added them. ...
written 4 months ago by Fatima610
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Comment: C: Extract fasta sequences based on ids file
... Hi, I think if you change `$0 ~ pattern` to `$1 ~ pattern` it will give you the right output. You can also try this one: cat id_file.txt | while read id; do grep -A 1 ">$id " seq-file.fasta >> output_file.fasta ; done Please make sure there's no empty lines in your files. Also I su ...
written 4 months ago by Fatima610
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Comment: C: Extract fasta sequence from multifasta file using id and position in range
... You can use the following code: cat id_file.txt | while read id start stop; do echo ">"$id >> output_file.fasta ; perl -ne 'if(/^>(\S+)/){$c=grep{/^$1$/}qw('$id')}print if $c' seq-file.fasta | tail -n +2 | cut -c $start-$stop >> output_file.fasta ; done To use this code * ...
written 4 months ago by Fatima610
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Comment: C: Help in using GenomicRanges from R to get neighbouring genes
... You might be able to modify this code or modify your input and get the result that you need: https://www.biostars.org/p/223443/#223457 This might not be efficient if your tables are large, but you can store both of your tables in one Table, and use the first column as an indicator of what table y ...
written 4 months ago by Fatima610

Latest awards to Fatima

Scholar 6 months ago, created an answer that has been accepted. For A: bash script for RNA seq analysis
Centurion 7 months ago, created 100 posts.
Scholar 7 months ago, created an answer that has been accepted. For A: bash script for RNA seq analysis
Scholar 8 months ago, created an answer that has been accepted. For A: bash script for RNA seq analysis
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Parsing gff files using python and awk
Popular Question 2.5 years ago, created a question with more than 1,000 views. For concatenating different columns of different files bash script
Scholar 3.0 years ago, created an answer that has been accepted. For A: bash script for RNA seq analysis
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: bash script for RNA seq analysis
Supporter 3.0 years ago, voted at least 25 times.

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