User: Fatima
Fatima • 590
- Reputation:
- 590
- Status:
- 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
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... **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
Fatima • 590
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... 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
Fatima • 590
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... `; done` was missing from two of my commands. I added them. ...
written 14 days ago by
Fatima • 590
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... 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
Fatima • 590
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... 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
Fatima • 590
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... 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
Fatima • 590
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... 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
Fatima • 590
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... 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
Fatima • 590
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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
Fatima • 590
0
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2
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96
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... 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
Fatima • 590
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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