User: Giovanni.madrigal12

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Posts by Giovanni.madrigal12

<prev • 27 results • page 1 of 3 • next >
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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 26 days ago by Giovanni.madrigal1290
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Comment: C: VCF file conversion to BayeScan format is not working
... Not sure if this is a good solution, but it is one that works. Assuming you performed a *De novo* analysis, you can change the quality scores in your vcf from "." to some arbitrary value and using the python script available [here][1]. You can do something along the lines of `awk -F '/t/' '{ if ($6 ...
written 11 weeks ago by Giovanni.madrigal1290
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Answer: A: how to make an input file for DAVID Bioinformatics Tool for wheat's RNA seq data
... A simple solution would be to BLAST your sequences, retrieve the gene ID's, and put them in a list. ...
written 3 months ago by Giovanni.madrigal1290
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Answer: A: Guildeline Required For Gene Ontology, after Differntial expression analysis
... Although you may need to may an account (which is free), [omictools][1] can be used to search for numerous bioinformatic programs that are designed for whatever task you have in mind. [1]: https://omictools.com/ ...
written 3 months ago by Giovanni.madrigal1290
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Answer: A: STRUCTURE software file format
... There is also a python script you can use, located [here][1]. [1]: https://github.com/ldutoit/personal_libraries/blob/master/standalonescripts/vcf2structure.py ...
written 3 months ago by Giovanni.madrigal1290
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Comment: C: Install trimmomatic on windows computer?
... If you want to skip the installation procedure, you can make a free account in [Galaxy][1], which has Trimmomatic and several other bioinformatic tools available. It is a great start if you are new to bioinformatics. [1]: https://usegalaxy.org/ ...
written 5 months ago by Giovanni.madrigal1290
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Comment: C: Difference between Private SNPs and Singleton SNPs
... A list of GATK's methods and algorithms can be found [here.][1] I hope this helps. [1]: https://software.broadinstitute.org/gatk/documentation/topic?name=methods ...
written 5 months ago by Giovanni.madrigal1290
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Comment: C: Advice on Blast output
... In the past, I have specified the XML output (-outfmt 5) and converted the results using this [python script.][1] This allows you to get a good amount of information per hit. [1]: https://github.com/peterjc/galaxy_blast/blob/master/tools/ncbi_blast_plus/blastxml_to_tabular.py ...
written 5 months ago by Giovanni.madrigal1290
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Comment: C: Difference between Private SNPs and Singleton SNPs
... I would assume the private alleles or SNPs were found during the clustering step of your analysis. I would need to know how you generated your VCF to give you a more accurate answer. ...
written 5 months ago by Giovanni.madrigal1290
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Answer: C: What kind of R Project I can do related to gene expression analysis or protein c
... If you're able to learn some command line to utilize tools like Salmon, DESeq would be a great tool to use. A workflow can be found [here.][1] [1]: https://master.bioconductor.org/help/course-materials/2015/LearnBioconductorFeb2015/B02.1.1_RNASeqLab.html ...
written 5 months ago by Giovanni.madrigal1290

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

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