User: ekwame

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ekwame60
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Posts by ekwame

<prev • 24 results • page 1 of 3 • next >
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Comment: A: Convert list of ensembl Human genes -GRCh38.p13- from biomart to hg38 coordinate
... thanks @genomax for the explanation. yes it seems these genes are also in the patches. what is usually done in the community? these are list of DNA repair genes which i want to the intersect with my `.VCFs` any suggestions on how to go about this correctly? ...
written 5 weeks ago by ekwame60
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Convert list of ensembl Human genes -GRCh38.p13- from biomart to hg38 coordinates
... Hi all, i download few ensensemble genes with cordinates (Human genes (GRCh38.p13)) from biomart and want to convert to ucsc hg38 cordinates. there are some contigs not in hg38 ref dictionary see this example (full file below); CHR_HSCHR5_1_CTG1_1 70376388 70411404 ENSG00000276910 GTF2H2 i did ...
genome ensembl hg38 liftover assembly written 5 weeks ago by ekwame60
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Answer: A: what is the difference between calling variants with and without interval list?
... Specifying an interval list restricts your variant calling to only regions in the interval list. by not specifying an interval list, you are calling variants across the whole genome hence the big size of your output file. interval list are particularly useful when for whole exomes sequence data whe ...
written 6 weeks ago by ekwame60
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filtered and dropped vcfs empty when filtering 1000 gemomes variants with Annova
... Hi I'm using annovar to filter germline variants by `--score_threshold` but nothing is either filtered or dropped. please I'm I missing something in the code? `perl annotate_variation.pl --filter /sc/hydra/projects/canan/Breast_Cancer/results/germline/new_germline07302020/Germline_108_07302020.vc ...
annovar germline annotation 1000genomes written 6 weeks ago by ekwame60
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Answer: C: [R] makeGRangesFromDataFrame errors that metadata columns (in dframe) has reserv
... Thanks @Kevin Blighe, it turns out the 'strand' column was the source of error. i think because of `ignore.strand=TRUE` flag in `GenomicRanges::makeGRangesFromDataFrame` set `ignore.strand=TRUE` inistially because `GenomicRanges::makeGRangesFromDataFrame` wasn't recognizing values in `strand` colu ...
written 3 months ago by ekwame60
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Comment: C: [R] makeGRangesFromDataFrame errors that metadata columns (in dframe) has reserv
... class(merged.biomart.hg19.cna) [1] "data.frame" typeof(merged.biomart.hg19.cna) [1] "list" str(merged.biomart.hg19.cna) 'data.frame': 57812 obs. of 24 variables: $ seqnames : Factor w/ 24 levels "1","10","11",..: 1 1 1 1 1 1 1 1 1 1 ... $ start ...
written 3 months ago by ekwame60
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[R] makeGRangesFromDataFrame errors that metadata columns (in dframe) has reserved words. this is not the case
... Hello Biostars, converting dataframe to Granges object using `GenomicRanges::makeGRangesFromDataFrame` but keeeps failing due to presumably reserved names in metadata column but my metadata columns do not contain these "seqnames", "ranges", "strand", "seqlevels", "seqlengths", "isCircular", "s ...
R bioconductor genomicranges written 3 months ago by ekwame60 • updated 3 months ago by Kevin Blighe65k
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Answer: A: Rename sample names in g.vcf files fails [Error Segmentation fault (core dumped)
... ouch! I forget to post my solution! just in case someone else encounters similar solution. `bcftools reheader --samples` requires a file with sample names so I specified correctly file in local directory by inserting quotes `"${sampleName}.txt"` to make it work. thanks everyone for the support S ...
written 3 months ago by ekwame60
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[R] subsetByOverlaps (Granges list and Granges object) not giving specific hits
... Dear Biostars, I have GRangesList object of length 15 with metadata (of gene annotations & copy number), created small GRanges object to use to query GrangeList by subsetByOverlaps. but subsetByOverlaps seem not working for GrnagesLists, results end being same as orginial GrangesList. has anyon ...
R bioconductor genomicfeatures written 3 months ago by ekwame60
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Comment: A: Rename sample names in g.vcf files fails [Error Segmentation fault (core dumped)
... I tried this second approach but results are printed to the screen; I'm not really sure what I'm doing wrong? gvcfs="/sc/hydra/projects/canan/colon_cancer10312019/joint_calling_colon/gvcfs/renamed_sm_gvcfs/*.hg38.g.vcf.gz" for i in $gvcfs do sampleName=`basename -s .hg38.g.vcf.gz ...
written 5 months ago by ekwame60

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