User: aarvaBioinfo

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aarvaBioinfo10
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Posts by aarvaBioinfo

<prev • 14 results • page 1 of 2 • next >
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single cell sequencing datasets batch effect
... hi all, I have 3 single cell sequencing datasets from different year and in the form of cell ranger output files as barcode.tsv, gene.tsv and matrix.mtx files for each sample then how can i remove batch effect from them for gene expression analysis. is anyone have experience for this ? ...
R written 4 months ago by aarvaBioinfo10
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Comment: C: SNPs genomic classification based on VCF annotation
... hi, cpad0112, I highly appreciate you for help. I gave just for example 10 and 0.5%. not calculated value. sorry due to confidential, I could not share vcf data. if i just keep table header as: CHROM POS SNP-ID Ref Alt Gene_name Gene_ID SNP_types or SNP-classification then it can be made usi ...
written 7 months ago by aarvaBioinfo10
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Comment: C: SNPs genomic classification based on VCF annotation
... hi, cpad0112, Thank you for your reply and valuable link. I will try this. beside as you asked for example vcf set so here is example of annotated vcf data as: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Chr01 85514 . G C 222.003 PASS VDB=0.0681475;SGB=-0.693021;MQSB ...
written 7 months ago by aarvaBioinfo10
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Comment: C: SNPs genomic classification based on VCF annotation
... hi cpad0112, Thank you very much for your help. my VCF file was annotated with snpEff and I found that some SNPs shows both "upstream" and "downstream_gene_region" in the same data line so do you have some idea how can I filter this and get exact count and percentage of SNPs with the Gene ID as "do ...
written 8 months ago by aarvaBioinfo10
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SNPs genomic classification based on VCF annotation
... Dear All, I want to make a list of SNPs associated to with genes in Genomic region as below : 1. downstream_gene_variant 2. upstream_gene_variant 3. synonymous_variant 4. Intron_variant 5. missense_variant 6. 5'-prime_UTR_variant 7. 3'-prime_UTR_variant using my "Annotated vcf file" by snpEff pro ...
R snp written 8 months ago by aarvaBioinfo10
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Sorting of SNPs which has less than 0.05 threshold P-Value
... How can we get total number of SNPs in plink association output file as "qassoc" and "adjusted file" which has less than 0.05 P values? ...
plink snp written 8 months ago by aarvaBioinfo10 • updated 8 months ago by zx87547.1k
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Creation of hapmap format file for multi samples using individual sample gVCF file REF/ALT info
... Hi all, I want to create a hapmap file for multi samples by using each samples genomic VCF file columns information as CHROME, POS, REF and ALT. Is anyone has idea about this using some script programs. here is my gVCF file examples: Sample1.gvcf Chr01 36230803 . T <*> 0 . DP=19;I16=1 ...
snp written 9 months ago by aarvaBioinfo10 • updated 9 months ago by Pierre Lindenbaum118k
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Comment: C: merging of multi samples tabix and bzipped vcf files into one vcf file using Per
... thank you JC for links. ...
written 9 months ago by aarvaBioinfo10
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Comment: C: merging of multi samples tabix and bzipped vcf files into one vcf file using Per
... Thank you cpad0112 for valuable links :) actually I need to do this by using Perl ...
written 9 months ago by aarvaBioinfo10
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merging of multi samples tabix and bzipped vcf files into one vcf file using Perl program.
... HI, I want to merge multi sample individual files ( vcf1.vcf.gz, vcf2.vcf.gz.............vcf30.vcf.gz) which has is tabix index and compressed by bgzipp so Is here anyone know the Perl Program for this. ...
perl vcf written 9 months ago by aarvaBioinfo10 • updated 9 months ago by JC7.7k

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