User: Giovanni.madrigal12

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Posts by Giovanni.madrigal12

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Comment: C: How to upgrade R version in ubuntu?
... I'm not quite sure what the error would be. If you followed all the instructions, it should have worked. ...
written 25 days ago by Giovanni.madrigal12130
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Comment: C: How to upgrade R version in ubuntu?
... What does your source.list look like? ...
written 25 days ago by Giovanni.madrigal12130
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Comment: C: How to upgrade R version in ubuntu?
... Make sure you have the correct repository for updating R. I also have Ubuntu 16.04 and changed my repository. Check your sources file found here `/ect/apt/sources.list`. I have `deb https://cloud.r-project.org/bin/linux/ubuntu xenial-cran35/`on my list and commented out `deb https://lib.stat.cmu.edu ...
written 26 days ago by Giovanni.madrigal12130
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Comment: C: How to upgrade R version in ubuntu?
... What version of Ubuntu are you using? This may be a repository issue if you are using Ubuntu 16.04 or older. ...
written 26 days ago by Giovanni.madrigal12130
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Answer: A: Running BWA mem in a for loop
... You can do something like `for i in $(ls -1 *R1.fq.gz | sed 's/\.R1.fq.gz//'); do bwa mem -t 16 /path/to/reference/genome/reference.genome.fa.gz $i\.R1.fq.gz $i\.R2.fq.gz | samtools view -Sb - | samtools sort -@ 16 -o $i\.bam - ; done` Hope this helps ...
written 4 weeks ago by Giovanni.madrigal12130
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Comment: C: Snakemake: Missing output files:
... Maybe try changing "->" to ">" in your shell command ? ...
written 8 weeks ago by Giovanni.madrigal12130
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Comment: C: QUAL scores in ipyrad vcf file output
... Not an answer towards your question, but you can ask for help directly from the developers [here][1] [1]: https://gitter.im/dereneaton/ipyrad ...
written 4 months ago by Giovanni.madrigal12130
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Comment: C: Counting number of hits of blastn output
... Can you do the above command on the column containing the database sequence itself? I don't think a query sequence would hit a database sequence twice, so that should let you see how many times the database sequence was hit, with the number of unique hits representing the number of query sequences. ...
written 4 months ago by Giovanni.madrigal12130
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Comment: C: Counting number of hits of blastn output
... Adding to this comment, cut -f1 | sort | uniq -c This will give you the number of hits each query sequence had. ...
written 5 months ago by Giovanni.madrigal12130
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Comment: C: The pStacks module of Stacks has been removed?
... Just for future reference, any questions on STACKS can be addressed in their google group found [here][1]. Very active community with Catchen himself being involved. [1]: https://groups.google.com/forum/#!forum/stacks-users ...
written 5 months ago by Giovanni.madrigal12130

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Teacher 11 months ago, created an answer with at least 3 up-votes. For A: STRUCTURE software file format

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