User: Fatima

gravatar for Fatima
Fatima590
Reputation:
590
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Trusted
Location:
United states
Twitter:
fsharifi4
Scholar ID:
Google Scholar Page
Last seen:
1 day ago
Joined:
3 years, 6 months ago
Email:
f************@gmail.com

Posts by Fatima

<prev • 192 results • page 1 of 20 • next >
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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 6 days ago by Fatima590
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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 14 days ago by Fatima590
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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 14 days ago by Fatima590
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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 14 days ago by Fatima590
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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 16 days ago by Fatima590
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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 16 days ago by Fatima590
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Comment: C: Bowtie-Build error ,Warning: Empty input file Reference file does not seem to be
... I think there's extra spaces between your directory and file names! Does your scaffold file contain scaffolds too? Because the one you posted seems to only contain headers. /GapFiller_v1-10_linux-x86_64/bowtie/bowtie-build --quiet --noref GapFiller_RESULTS/alignoutput/GapFiller_RESULTS.1.g ...
written 5 weeks ago by Fatima590
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Comment: C: Unable to perform merging through cuffmerge
... in the directory with `transcripts.gtf` you can use the command `pwd` to get the path to that directory. https://www.redhat.com/sysadmin/basic-linux-commands ...
written 5 weeks ago by Fatima590
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Comment: C: awk gsub question
... cat in.txt | sed 's/A/@@@/g' | sed 's/B/###/g' | sed 's/C/%%%/g' > out.txt and as @ATpoint mentioned: cat in.txt | awk '{gsub("A","@@@");gsub("B","###");gsub("C","%%%");print}' > out.txt ...
written 5 weeks ago by Fatima590
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Answer: A: Sugestion for circular visualization of genome
... https://software.broadinstitute.org/software/igv/ http://jonathancrabtree.github.io/Circleator/index.html https://www.sanger.ac.uk/science/tools/dnaplotter ...
written 5 weeks ago by Fatima590

Latest awards to Fatima

Scholar 8 weeks ago, created an answer that has been accepted. For A: bash script for RNA seq analysis
Centurion 3 months ago, created 100 posts.
Scholar 3 months ago, created an answer that has been accepted. For A: bash script for RNA seq analysis
Scholar 3 months ago, created an answer that has been accepted. For A: bash script for RNA seq analysis
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Parsing gff files using python and awk
Popular Question 2.1 years ago, created a question with more than 1,000 views. For concatenating different columns of different files bash script
Scholar 2.6 years ago, created an answer that has been accepted. For A: bash script for RNA seq analysis
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: bash script for RNA seq analysis
Supporter 2.7 years ago, voted at least 25 times.

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