User: kmkdesilva

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kmkdesilva90
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Posts by kmkdesilva

<prev • 52 results • page 1 of 6 • next >
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Number of reads in the downloaded fastq file
... Hi, I am trying to download some data from SRA. I used fasterq-dump. This is the command I used. fasterq-dump --split-files --split-spot -O /path/fastq SRR3045676 I wanted to check whether I have downloaded all the reads for the accession. When I used vdb-dump it showed there are 166,306,903 seq ...
sra vdb-dump --info read count fasterq-dump written 8 days ago by kmkdesilva90
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Comment: C: Does bedtools intersect output overlaps with isoforms?
... Sorry, my inputs are in bed file format. Thank you ...
written 5 weeks ago by kmkdesilva90
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Does bedtools intersect output overlaps with isoforms?
... Hi I am using bedtools intersect option to identify which regions in my file are overlapping with exons. One thing I am curious about, is if a gene has 5 isoforms with an exon common to each, does bedtools return all 5 for the overlap, or just 1? ...
bedtools isoforms written 5 weeks ago by kmkdesilva90 • updated 4 weeks ago by Kevin Blighe66k
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Comment: C: Sort a bed file
... Perfect. Thank you very much for sharing Jorge. ...
written 5 weeks ago by kmkdesilva90
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Comment: C: Sort a bed file
... Thank you Kevin. -u also did the job. ...
written 5 weeks ago by kmkdesilva90
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Comment: C: Sort a bed file
... Thank you very much Kevin. If I add -u option to this command 'sort -k1,1 -k2,2n -V test.bed chr1' will I get both sorted and unique records? ...
written 5 weeks ago by kmkdesilva90
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(Closed) Sort a bed file
... Hi I tried to sort a bed file using *bedtools*. It sorted the chromosomes in, chr1 chr10 chr11 chr12 . . chr19 chr2 chr20 Please tell me how I can sort the bed file in `chr1, chr2. chr3 ..... chrX` order? ...
bedtools bed file sort written 5 weeks ago by kmkdesilva90 • updated 5 weeks ago by zx87549.7k
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Comment: A: How to get input for provean from vcf files annotated by snpeff?
... Hi @shl198 I have the same issue did you find a solution ...
written 6 weeks ago by kmkdesilva90
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expected heterozygosity, observed heterozygosity and excesshet key in vcf format
... Hi, What is the relationship between expected heterozygosity (He), observed heterozygosity (Ho) and ExcessHet key in vcf info field? ...
vcf excesshet heterozygosity written 8 weeks ago by kmkdesilva90
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Error while running gatk CombineGVCFs
... Hi everyone, I am trying to combine 35 gvcf files. I used gatk/4.1.3.0 CombineGVCFs to do this. I used the format given in their website. gatk CombineGVCFs \ -R reference.fasta \ --variant sample1.g.vcf.gz \ --variant sample2.g.vcf.gz \ -O cohort.g.vcf.gz my comma ...
gatk combinegvcf user error written 3 months ago by kmkdesilva90 • updated 3 months ago by Pierre Lindenbaum131k

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