User: O.rka

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O.rka30
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Posts by O.rka

<prev • 34 results • page 1 of 4 • next >
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Comment: C: How to get SNP identifiers from VCF file?
... It errored when I tried both the full and trimmed VCFs ...
written 3 hours ago by O.rka30
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Comment: C: How to get SNP identifiers from VCF file?
... I ended up running `vcf2bed` and then: `bedmap --echo --echo-map-id --delim '\t' hg38.snp147.bed genome.bed > genome.vcf.hg38.snp147.bed` and it worked. Do you know of any way I can map the rs* IDs to their descriptive names? ...
written 3 hours ago by O.rka30
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Comment: C: How to get SNP identifiers from VCF file?
... I ran it on the grid and got the following error: qsub -cwd -V -N sift "SnpSift annotate -id 00-All.vcf genome.vcf > genome.dbSNP.hg38.annotated.vcf" Exception in thread "main" java.lang.OutOfMemoryError: Java heap space at java.util.Arrays.copyOf(Arrays.java:3284) at org.snpsi ...
written 22 hours ago by O.rka30
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Comment: C: How to get SNP identifiers from VCF file?
... Do you know if this takes the truncated VCF that I've previewed above? or full VCFs only? ...
written 23 hours ago by O.rka30
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Comment: C: How to get SNP identifiers from VCF file?
... Do you have any example commands you would use? ...
written 23 hours ago by O.rka30
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Comment: C: How to get SNP identifiers from VCF file?
... I'm trying it out with SnpSift right now. Do you have any examples of its use with bcftools? ...
written 23 hours ago by O.rka30
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Comment: C: How to get SNP identifiers from VCF file?
... I first ran this: LC_ALL=C wget -qO- http://hgdownload.cse.ucsc.edu/goldenpath/hg38/database/snp147.txt.gz \ | gunzip -c \ | awk -v OFS="\t" '{ print $2,$3,($3+1),$5 }' \ | sort-bed - \ > hg38.snp147.bed and then ran my non-trimmed (all the columns) vcf file ` ...
written 23 hours ago by O.rka30
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How to get SNP identifiers from VCF file?
... I grabbed the first couple of columns from my whole genome VCF file. It looks like this. Are there any tools either web-based, Python, or R that I could use to get SNP identifiers (e.g. `rs429358` or `rs7412`) for all of my SNPs that are in a particular database? I'm very new to working with VCF f ...
vcf genome database snp clinical written 1 day ago by O.rka30 • updated 1 day ago by Denise - Open Targets4.2k
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Do counts need to be filtered for edgeR to properly work on metatranscriptome?
... I want to use edgeR to look at differential gene expression. I have a metatranscriptome `m= 1 221 663` ORFs and `n= 83 samples` with `(m= 34 control, and m= 49 experimental)` samples. I can trim out many of these ORFs if necessary to include only ORFs that have hits in at least 75% of the samples ...
metatranscriptomics metagenomics rna-seq edger written 14 days ago by O.rka30
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Where to download gff3 file for EcoCyc data?
... I'm looking for a gff3 file with EcoCyc IDs. Do I need to just download the version from Ensembl and then convert the IDs? Alternatively, is there a flat file from EcoCyc that has the positions of all of the genes in E. coli? ...
gff3 assembly genes ecoli written 6 weeks ago by O.rka30

Latest awards to O.rka

Popular Question 12 weeks ago, created a question with more than 1,000 views. For Differential Gene Expression (EdgeR?) : What are the steps in computing this?
Supporter 11 months ago, voted at least 25 times.
Popular Question 12 months ago, created a question with more than 1,000 views. For How to tell bloodtype from SNPs data?
Student 18 months ago, asked a question with at least 3 up-votes. For Most up-to-date Gene Ontology [GO] analysis?

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