User: gaelgarcia05

gravatar for gaelgarcia05
gaelgarcia05190
Reputation:
190
Status:
Trusted
Location:
UK
Last seen:
4 months, 3 weeks ago
Joined:
6 years, 5 months ago
Email:
c**********@gmail.com

Posts by gaelgarcia05

<prev • 56 results • page 1 of 6 • next >
0
votes
4
answers
1.5k
views
4
answers
Answer: A: how to produce plots like this in R
... This is from the Seurat `DotPlot` function, which is documented here: https://github.com/satijalab/seurat/blob/master/R/plotting.R Essentially, it is a ggplot `geom_point` plot. ...
written 4 months ago by gaelgarcia05190
0
votes
2
answers
3.9k
views
2
answers
Comment: C: Finding Variable Genes in Seurat, scRNA-seq
... Hi @igor , @lishen0709 – did you find a solution to your question about selecting the correct parameters for x and y cutoffs in Seurat's FindVariableGenes? Thanks! ...
written 8 months ago by gaelgarcia05190
0
votes
0
answers
595
views
0
answers
Comment: C: Compare allele frequency of SNPs in my data to their allele frequency in differe
... Thanks @finswimmer - just updated my post to clarify what I'm looking for as output. The output table I have in mind would look something like this: snpID MAF_mysamples MAF_european MAF_finnish MAF_african MAF_se_asian MAF_asian ...
written 12 months ago by gaelgarcia05190
0
votes
2
answers
27k
views
2
answers
Comment: C: How To Find Major And Minor Alleles From Dbsnp ?
... Thank you for your thorough explanation, Jorge — Are the populations and MAFs per population in the `Population Diversity` table those corresponding to the 1000 Genomes project, or has this table been updated to include ExAC populations and MAFs? ...
written 12 months ago by gaelgarcia05190
0
votes
0
answers
1.4k
views
0
answers
Comment: C: tools to calculate Exac population specific frequency
... Hi Jan, Wondering if you ended up finding an effective way to do this? I'm currently trying to do the same thing — except I don't relally understand what you mean by 'MAF files'. ...
written 12 months ago by gaelgarcia05190
4
votes
0
answers
595
views
0
answers
Compare allele frequency of SNPs in my data to their allele frequency in different human populations - ExAC vs 1000 Genomes vs Other?
... Hello, I have a list of SNPs (in the form of a VCF) found in our [very] targeted sequencing dataset of ~15,000 individuals. I am looking to compare the MAFs of these SNPs within this 'population' (our dataset) to their MAFs across different populations, such as the populations defined in ExAC or t ...
maf 1000genomes exac snp sequencing written 12 months ago by gaelgarcia05190
0
votes
0
answers
4.1k
views
0
answers
Comment: C: Converting VCF to PLINK .bed binary fileset to check for pedigree errors with KI
... Ahh, that explains so much! Thanks! ...
written 13 months ago by gaelgarcia05190
0
votes
5
answers
28k
views
5
answers
Comment: C: How To Convert Vcf File To Plink Ped Format?
... @alolex, Do you do this using the above mentioned tool from GATK `VariantsToBinaryPed`? Or with PLINK's --make-bed? ...
written 13 months ago by gaelgarcia05190
0
votes
0
answers
4.1k
views
0
answers
Comment: C: Converting VCF to PLINK .bed binary fileset: How do the different tools availabl
... Hello again, I guess I'm still confused about the right way to go about this -- have not been able to get past the VCF/.fam mismatch error. I'm not sure that the options suggested for interpreting the VCF sampleIDs will help my particular case (`--double-id`, `--id-delim`, `--const-fid`) - The trou ...
written 13 months ago by gaelgarcia05190
0
votes
0
answers
4.1k
views
0
answers
Comment: C: Converting VCF to PLINK .bed binary fileset: How do the different tools availabl
... Kevin - Do the sample IDs in the VCF ***have*** to include both FID and IID? My VCF Sample IDs consist of only the IID -- I'm still getting an error message after filtering the .fam file to contain only samples found in the VCF, in addition to specifying the order with an IDsort file. ./plink ...
written 13 months ago by gaelgarcia05190

Latest awards to gaelgarcia05

Great Question 12 months ago, created a question with more than 5,000 views. For Why Am I Getting So Many Unmapped Reads In Star, Classified As "Too Short"?
Scholar 13 months ago, created an answer that has been accepted. For A: Full list of KING options and paramenters
Appreciated 5.9 years ago, created a post with more than 5 votes. For Why Am I Getting So Many Unmapped Reads In Star, Classified As "Too Short"?
Great Question 5.9 years ago, created a question with more than 5,000 views. For Why Am I Getting So Many Unmapped Reads In Star, Classified As "Too Short"?
Good Question 5.9 years ago, asked a question that was upvoted at least 5 times. For Why Am I Getting So Many Unmapped Reads In Star, Classified As "Too Short"?
Popular Question 5.9 years ago, created a question with more than 1,000 views. For Why Am I Getting So Many Unmapped Reads In Star, Classified As "Too Short"?
Popular Question 5.9 years ago, created a question with more than 1,000 views. For Which Strand Of The Mrna Molecule Does The Sequencer Output As A "Read"?
Popular Question 5.9 years ago, created a question with more than 1,000 views. For What Happened To -K In Tophat For Multiple-Mapping Reads?
Popular Question 5.9 years ago, created a question with more than 1,000 views. For Split A Bam File Into Smaller Files By Tile Number
Popular Question 5.9 years ago, created a question with more than 1,000 views. For Does Tophat Use The Library-Type Information For Mapping, Or Just For The Xs Flag?
Popular Question 5.9 years ago, created a question with more than 1,000 views. For Deseq Standard Comparison Or Multifactorial / Model Fitting?
Popular Question 5.9 years ago, created a question with more than 1,000 views. For Local Alignment Of Short Reads: Mosaik, Bowtie2, Bwa?
Popular Question 5.9 years ago, created a question with more than 1,000 views. For How Do Tophat Options -G , --Supress-Hits, And Bowtie Options Interplay?
Popular Question 5.9 years ago, created a question with more than 1,000 views. For Purpose Of Y-Shaped Adapters In Illumina Sequencing?
Supporter 5.9 years ago, voted at least 25 times.
Student 5.9 years ago, asked a question with at least 3 up-votes. For Why Am I Getting So Many Unmapped Reads In Star, Classified As "Too Short"?
Student 5.9 years ago, asked a question with at least 3 up-votes. For Does Tophat Use The Library-Type Information For Mapping, Or Just For The Xs Flag?
Autobiographer 5.9 years ago, has more than 80 characters in the information field of the user's profile.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1545 users visited in the last hour