User: Giovanni.madrigal12

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Posts by Giovanni.madrigal12

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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 7 hours ago by Giovanni.madrigal1240
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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 3 days ago by Giovanni.madrigal1240
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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 3 days ago by Giovanni.madrigal1240
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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 3 days ago by Giovanni.madrigal1240
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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 3 days ago by Giovanni.madrigal1240
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Comment: C: Difference between Private SNPs and Singleton SNPs
... If I am interpreting this correctly, private SNPs are SNPs private in regards to a population, or in your case, a family. Singleton SNPs would be SNPs that only show up once in a single individual. Hope this helps. ...
written 3 days ago by Giovanni.madrigal1240
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Comment: C: how to filter 3 variants files (in excel format) simultaneously?
... You can make a list using the POS column using awk, filter with uniq, and search the child file like this cat het_parent1.xlsx het_parent2.xlsx | awk '{print $2}' | uniq > List.txt cat child.xlsx | grep -f List.txt | awk '{ if ($9 ~ "HOM") print $0 }' > hom_child.xlsx ...
written 19 days ago by Giovanni.madrigal1240
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Comment: C: how to filter 3 variants files (in excel format) simultaneously?
... You can do a simple extraction using awk for each file. The commands will look something like this awk '{ if ($9 ~ "HET") parents.xlsx print $0 }' > het_parents.xlsx awk '{ if ($9 ~ "HOM") child.xlsx print $0 }' > hom_child.xlsx ...
written 19 days ago by Giovanni.madrigal1240
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Comment: C: How to merge multiple VCF files (each has multiple samples genotype) from differ
... More details on what commands you are using and errors would be helpful. I am aware of another post with the same issue [Merge individual vcf files][1]. There is also another tool kit called vcflib (https://github.com/vcflib/vcflib) if you would care to test your data there. [1]: http://seqanswe ...
written 10 weeks ago by Giovanni.madrigal1240
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Comment: C: How meaningful is GO term enrichment of SNP outliers when only a small proportio
... I don't know if this is relevant at this point in time, but it is to my knowledge that RAD-seq may not be appropriate for GO term analysis. RAD-seq is used to generate genomic data, not transcriptomic data. Genomic data does not necessarily reflect what genes an organism is expressing. In short, RAD ...
written 10 weeks ago by Giovanni.madrigal1240

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