User: nadiabeg.comsats

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Posts by nadiabeg.comsats

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How to extract uniquely aligned paired end reads obtained from freebayes using diffrent parmeter combinations of samtools?
... I have 10x reads and I need uniquely aligned reads for SNP calling. I am using samtools to extract uniquely aligned reads but I am not satisfied by the results. It would be great if someone can share the exact way of filtering these reads. I tried many combinations and checked many sources online bu ...
ngs read filtering samtools freebayes written 3 months ago by nadiabeg.comsats0
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Variant calling and alignment stats
... Hi. I am using samtools flagstats to see the statistics of my alignment file. It looks something like this: I have 10x genomics reads. `575130408 + 0 in total (QC-passed reads + QC-failed reads) 36759786 + 0 secondary 0 + 0 supplementary 114890896 + 0 duplicates 553 ...
alignment snp written 5 months ago by nadiabeg.comsats0
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nucleotide blast of flanking sequences around SNPs
... Hi, I have some SNPs with flanking sequences ~60 kb both upstream and downstream of a SNP. The flanking sequence looks some thing like this. ATTATGGCT[A/T]TTAGCTTA (this is just an example). My question is 1) I am making my own fasta file by using this information and converting aforementioned seque ...
nblast snp written 5 months ago by nadiabeg.comsats0 • updated 5 months ago by David Gortler20
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Comment: C: Flanking sequence retreival
... thanks, but I have to pick variant location from vcf file and it contains millions of variants. I am not sure how long will it takes to fetch sequence for each variant position. ...
written 9 months ago by nadiabeg.comsats0
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Comment: C: Flanking sequence retreival
... I guess bedtools flank gives only intervals not complete sequence present around a given variant. ...
written 9 months ago by nadiabeg.comsats0
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Comment: C: Extract SNPs flanking sequences based on VCF and genome Fasta files
... Hi Denis, I used following code to do exactly what you are doing using pysam. Problem is my code is not very fast for bigger genomes. So I switched to the aforementioned code posted by you. It works when you set a lower flank score. Suppose I need a flanking sequence of 500bp on 5' ......pos......3' ...
written 9 months ago by nadiabeg.comsats0
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Flanking sequence retreival
... Hi all, I have a genome of size 7190 mb. I am using following python code to extract the flanking sequence nucleotide sequence around a list of variants. My code works for a smaller genome but it takes so long to process and fetch the sequence from a fasta file. Is there any way to speed up the pro ...
fasta sequence extraction variants written 9 months ago by nadiabeg.comsats0 • updated 9 months ago by finswimmer13k
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Bi-allelic SNP filtering
... Hi all, I am trying to get bi-allelic snps from my vcf file. I have a combined vcf file for 8 samples having tetraploid genomes. For getting bi-allelic markers I am using following command. bcftools view -m2 -M2 -v snps input.vcf.gz After filtering I am getting some weird marker entries as well suc ...
tetraploid genome bcftools bi-allelic snps written 9 months ago by nadiabeg.comsats0 • updated 9 months ago by Pierre Lindenbaum131k
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Filtering variants on the basis of average depth plus 3 standard deviation
... Hi all. I am working on variant filtration for my vcf file and found following parameters in one paper . To get high quality SNP they filtered variants on 1) raw read depth (DP) average sequence depth multiplied by the number of accessions; and 2) DP lower than average DP plus three standard deviat ...
variant filtering ngs variants written 9 months ago by nadiabeg.comsats0
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How to create snpEff data base for newly assembled genome?
... Hi all, I have my own de-novo assembled reference genome and gff file. I aligned my data on newly assembled reference genome. I have now some SNPs. I want to annotate these snps using snpeff to know about the genes linked with these SNPs. The problem is database creation for snpeff. I am not able t ...
genome snp written 10 months ago by nadiabeg.comsats0

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