User: Tawny

gravatar for Tawny
Tawny110
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110
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United States
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1 week, 1 day ago
Joined:
5 years, 7 months ago
Email:
m***********@battelle.org

Posts by Tawny

<prev • 19 results • page 1 of 2 • next >
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Comment: C: How to run a set or batch of genome assemblies at once in one go?
... @Philipp Bayer Thank you for your example. I was able to apply this to another program (UPARSE fastq_mergepairs) using a directory of over 700 files. This saved me a lot of time. ...
written 15 days ago by Tawny110
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Comment: C: Venter Genome Vcf
... The link above appears to be broken. Does anyone have the new link? ...
written 6 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 7 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 8 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 9 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 16 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 17 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 17 months ago by Tawny110 • updated 16 months ago by DCGenomics290
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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 2.1 years ago by Tawny110 • updated 9 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 3.2 years ago by Tawny110

Latest awards to Tawny

Popular Question 6 months ago, created a question with more than 1,000 views. For Is There Any File That Links The Enzyme Comission Number To Gi Numbers?
Good Question 16 months ago, asked a question that was upvoted at least 5 times. For What Is The Refseq Id For Illumina Phix Control?
Great Question 2.1 years ago, created a question with more than 5,000 views. For What Is The Refseq Id For Illumina Phix Control?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For What Is The Refseq Id For Illumina Phix Control?
Appreciated 3.2 years ago, created a post with more than 5 votes. For What Is The Refseq Id For Illumina Phix Control?
Student 3.2 years ago, asked a question with at least 3 up-votes. For What Is The Refseq Id For Illumina Phix Control?
Popular Question 5.2 years ago, created a question with more than 1,000 views. For What Is The Refseq Id For Illumina Phix Control?
Popular Question 5.2 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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