User: Giovanni.madrigal12

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Posts by Giovanni.madrigal12

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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 24 days ago by Giovanni.madrigal12110
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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 6 weeks ago by Giovanni.madrigal12110
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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 7 weeks ago by Giovanni.madrigal12110
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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 9 weeks ago by Giovanni.madrigal12110
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Comment: C: Qimme 2 analysis demultiplexing of fastq files
... This [thread][1] may help. [1]: https://www.biostars.org/p/204120/ ...
written 12 weeks ago by Giovanni.madrigal12110
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Comment: C: SNP input data for Arlequin
... What is your issue? I have ran across the issue of Arlequin not showing any progress during an analysis, and just had the analysis done in [DnaSP][1] instead. [1]: http://www.ub.edu/dnasp/ ...
written 12 weeks ago by Giovanni.madrigal12110
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Comment: C: Stacks error:failed to gz-open
... For future reference, whenever you have an issue running STACKS, you can look for a solution or post your issue in the STACKS google [group][1]. Julian Catchen is very good at providing assistance. [1]: https://groups.google.com/forum/#!forum/stacks-users ...
written 3 months ago by Giovanni.madrigal12110
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Comment: C: blastp command line not reporting hits
... Not sure if this will solve your issue, but these two papers may help you understand your issue a bit more. [Paper1][1] [Paper2][2] [1]: https://academic.oup.com/bioinformatics/article/35/9/1613/5106166 [2]: https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bt ...
written 3 months ago by Giovanni.madrigal12110
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Comment: C: STRING and PANTHER couldn't identify Uniprot accessions
... What kind of organism are you working with? Although PANTHER has a variety of organisms in their database listed [here][1], it just may be that your protein IDs are not listed in their database. [1]: http://pantherdb.org/panther/summaryStats.jsp ...
written 3 months ago by Giovanni.madrigal12110
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Answer: A: Uneven amount of total sequences across individuals in RAD-seq dataset
... You may find this [paper][1] interesting. A second read can also be found [here][2]. [1]: https://academic.oup.com/sysbio/article/66/3/399/2682283 [2]: https://bmcresnotes.biomedcentral.com/articles/10.1186/1756-0500-7-841 ...
written 4 months ago by Giovanni.madrigal12110

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Teacher 7 months ago, created an answer with at least 3 up-votes. For A: STRUCTURE software file format

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