User: MAPK

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MAPK1.5k
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Posts by MAPK

<prev • 506 results • page 1 of 51 • next >
9
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How to cite datasets downloaded from Ensembl?
... I am using datasets available here (GFF and Gene sequences): - https://plants.ensembl.org/Glycine_max/Info/Index Could someone please let me know how I could cite the source of this data? ...
ensembl citation written 29 days ago by MAPK1.5k • updated 28 days ago by Astrid_Ensembl270
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71
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Comment: C: GFF file for soybean RNAseq analysis
... Thank you. I ended up using NCBI's: https://www.ncbi.nlm.nih.gov/genome/?term=txid3847[Organism:noexp] ...
written 7 weeks ago by MAPK1.5k
2
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1
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71
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GFF file for soybean RNAseq analysis
... I am trying to do RNA-seq analysis for soybean datasets. I was looking at soybase (link: https://soybase.org/dlpages/#datastore ), but couldn't find the associated gff files. Could someone please direct me to the right gff files. Thank you for your help in advance. ...
rna-seq written 7 weeks ago by MAPK1.5k • updated 7 weeks ago by Brice Sarver3.5k
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Comment: C: How to decide on a reasonable title for a bioinformatics talk
... Thank you for your suggestion. It is for a job interview and I am trying to highlight my expertise in bioinformatics. ...
written 3 months ago by MAPK1.5k
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How to decide on a reasonable title for a bioinformatics talk
... As a bioinformatics researcher, I have been working on plants, animals and human genomes for past several years. I have been working on a wide array of datasets including exome genotyped data, small RNAs/RNAseq and microbiome datasets, and have published several papers based on these analyses. Howev ...
interview job bioinformatics talk written 3 months ago by MAPK1.5k • updated 3 months ago by Mensur Dlakic4.2k
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250
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Comment: C: IBD calculation with Plink
... Hi Chris, `./plink2 --make-bed --vcf test.vcf --maf 0.05 --out test.vcf` only creates `test.vcf.fam`, but not .bim and .bed files. Do I have to do `make-just..` for bim and bed files? ...
written 4 months ago by MAPK1.5k
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IBD calculation with Plink
... It's been a while since I last used Plink to calculate IBS/IBD. For a given VCF file, `test.vcf`, I did maf filtering and calculated IBD with these commands: plink --vcf test.vcf --maf 0.05 --recode --out test.vcf plink --file test.vcf --genome Do I also need to do Hardy-Weinberg or any o ...
plink ibd written 4 months ago by MAPK1.5k • updated 4 months ago by chrchang5236.7k
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Comment: C: How to properly get BED regions coverage
... @ATpoint `qualimap bamqc -bam file.bam -gff file.bed outformat PDF --java-mem-size=4G` gives me error: `Found 50 regions Filling region references... Failed to run bamqc java.lang.RuntimeException: BED format error, there should be at least 6 fields. Problematic line:` I was provided a bed file wi ...
written 4 months ago by MAPK1.5k
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Comment: C: Potential post-doc PI giving exam as part of hiring process
... This is a postdoc position in a 15-25th ranked medical school in the US. ...
written 5 months ago by MAPK1.5k
2
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2
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223
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2
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How to find virus sequence with no accession information?
... I am trying to retrieve the genomic sequence of HEV71 strain VR1432 used in this study (https://www.sciencedirect.com/science/article/pii/S1074761317302224?via%3Dihub), but could not find it. I would really appreciate if someone could guide me through the appropriate resources/link. Thanks ...
genome hev71 written 9 months ago by MAPK1.5k • updated 9 months ago by genomax80k

Latest awards to MAPK

Great Question 5 days ago, created a question with more than 5,000 views. For What are the terms for reference allele and alternate alleles in cancer?
Popular Question 16 days ago, created a question with more than 1,000 views. For Methods to correct for population stratification
Epic Question 16 days ago, created a question with more than 10,000 views. For R programming, concatenate or combine all the column contents
Popular Question 23 days ago, created a question with more than 1,000 views. For Methods to correct for population stratification
Great Question 26 days ago, created a question with more than 5,000 views. For What are the terms for reference allele and alternate alleles in cancer?
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Methods to correct for population stratification
Great Question 7 weeks ago, created a question with more than 5,000 views. For R programming, concatenate or combine all the column contents
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Reverse translate and get the genomic position
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Complete Genomics data analysis, pipeline version and batch effect
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Epic Question 10 weeks ago, created a question with more than 10,000 views. For R programming, concatenate or combine all the column contents
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Commentator 3 months ago, created a comment with at least 3 up-votes. For C: How to split vcf file by chromosome?
Great Question 3 months ago, created a question with more than 5,000 views. For R programming, concatenate or combine all the column contents
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Great Question 5 months ago, created a question with more than 5,000 views. For R programming, concatenate or combine all the column contents
Popular Question 5 months ago, created a question with more than 1,000 views. For Methods to correct for population stratification

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