User: Tawny

gravatar for Tawny
Tawny110
Reputation:
110
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Trusted
Location:
United States
Last seen:
3 months ago
Joined:
5 years, 3 months ago
Email:
m***********@battelle.org

Posts by Tawny

<prev • 18 results • page 1 of 2 • next >
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Comment: C: Venter Genome Vcf
... The link above appears to be broken. Does anyone have the new link? ...
written 3 months ago by Tawny110
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Comment: C: miniasm GFA format : first field - 'x' and 'a' line
... Did anyone ever find the answer to this? I too have miniasm output with the same a and x rows. ...
written 3 months ago by Tawny110
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Comment: C: Error with reading fasta file into R - "arguments imply differing number of rows
... I have seen this error in R before with other tasks I have done. I would start by making sure your fasta file is properly formatted. Is each amino acid sequence only on one line (not a multiline fasta)? Are there no blank lines in the fasta file? Is the line ending character compatible; Windows ...
written 4 months ago by Tawny110
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Comment: C: Has any one created a MetaSIM error profile file (.mconf) for Illumina reads >10
... I ended up using the error profile that is provided with MetaSIM and just expanding it. So I added new rows with similar values until I reached the read length I needed for my project. Then I plotted my revised profile file so I could look at it and make sure it looked like what I would expect for ...
written 5 months ago by Tawny110
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Comment: C: How can I retrieve the Protein 'name' using my BLAST tab delimited results?
... @5heikki thank you for the efetch command. I am just getting back to this problem after working on some other projects. I was able to include the second efetch command you posted into a Perl script and it is working nicely. It is slow but does the job. ...
written 12 months ago by Tawny110
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Comment: C: How can I retrieve the Protein 'name' using my BLAST tab delimited results?
... Both @5heikki and @genomax2 are correct. If the -outfmt stitle had been used my problem would have already been solved. BLAST+ can give me what I need. But in this instance I do not have the database that was used to generate this BLAST output. I am running the blastdbcmd using a database that I ...
written 13 months ago by Tawny110
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How can I retrieve the Protein 'name' using my BLAST tab delimited results?
... I have a file of BLAST protein results. It is over 100000 lines long. I want to get the protein/gene title associated with each accession number. I have been looking for a file I could search through similar to gene2refseq that would have the protein title mapped to the GI or accession with no lu ...
perl gene bioperl protein blast written 13 months ago by Tawny110 • updated 12 months ago by DCGenomics280
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Has any one created a MetaSIM error profile file (.mconf) for Illumina reads >100bp?
... I am considering using MetaSIM to create a metagenomic synthetic reads dataset.  I want to use an Illumina error profile.  I see that MetaSIM includes Illumina error profile files for 36bp and 80bp read lengths.  In their manual they say you can create your own error profile, the .mocnf file.  I nee ...
error profile illumina metagenomics metasim written 21 months ago by Tawny110 • updated 5 months ago by beacamara0
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Comment: C: Is there a list of available keywords for BioPerl?
... @SES  Thank you for taking the time to write such a complete response!  Exactly what I need! ...
written 2.9 years ago by Tawny110
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Is there a list of available keywords for BioPerl?
... I would like to better utilize the functionality available through Bio Perl.  I have not been able to find a list of available keywords to use to access different data when using something like Bio::SeqIO.  Does anyone have a list like this or can anyone point me to where I would find it?  For examp ...
perl bio perl bio::seqio written 2.9 years ago by Tawny110 • updated 2.9 years ago by SES7.9k

Latest awards to Tawny

Good Question 12 months ago, asked a question that was upvoted at least 5 times. For What Is The Refseq Id For Illumina Phix Control?
Great Question 21 months ago, created a question with more than 5,000 views. For What Is The Refseq Id For Illumina Phix Control?
Popular Question 21 months ago, created a question with more than 1,000 views. For What Is The Refseq Id For Illumina Phix Control?
Appreciated 2.9 years ago, created a post with more than 5 votes. For What Is The Refseq Id For Illumina Phix Control?
Student 2.9 years ago, asked a question with at least 3 up-votes. For What Is The Refseq Id For Illumina Phix Control?
Popular Question 4.9 years ago, created a question with more than 1,000 views. For What Is The Refseq Id For Illumina Phix Control?
Popular Question 4.9 years ago, created a question with more than 1,000 views. For What Is The Refseq Id For Illumina Phix Control?

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