User: taniamahmood38

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Posts by taniamahmood38

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MSA and phylogenetic tree for WGS data of mammalian species
... Hiii.... i want to do multiple sequence alignment to get format compatible for constructing a phylogenetic tree using whole genomes of mammalian species (i have whole genomes in FASTA format). Is there any tool on galaxy main or on galaxy europe that could do such high computational analysis robustl ...
msa galaxy phylogenetic tree written 21 days ago by taniamahmood380
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FastQC: Whisker plot interpretation-upper and lower quartile values l
... Hiii, i have a bit problem while interpreting Whisker plot from FASTQC tool which i got from bam dataset. I have a plot which has same upper and lower quartile value for a single base. Is it possible that upper and lower quartile value for a single base could be same ? Thanks!!! ...
quartile value fastqc galaxy whisker plot written 6 weeks ago by taniamahmood380
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Interpreting GT field in allelic form
... Hii, i have a bit problem while interpreting a genotype file when i come up with reading allelic form written as homozygous for the reference. My question is when i have a variant in my sample then why allele appears as homozygous for the reference. It should be either 0/1 or 1/1 for my sample. ...
galaxy next-gen allele vcf genotype written 6 weeks ago by taniamahmood380
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visualizing a VCF dataset
... Hiiii, i have made a vcf file and has filtered SNPs from there. Now, the problem is i am trying to visualize all these SNPs together on a window screen using trackster. But they are not appearing together at a time. Could anyone know the alternative visualization to ...
galaxy visualize vcf trackster snp written 7 weeks ago by taniamahmood380
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Answer: A: VCF to Interval dataset
... I am doing variant calling on my data and needed an interval file for several analysis in variant calling as input that's why i was stuck there. But now i have done with it by following your rejoinder thanks a lot. ...
written 8 weeks ago by taniamahmood380
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VCF to Interval dataset
... Could anyone tell me how to convert a VCF dataset into Interval dataset on main galaxy? Thanks!!! ...
galaxy tabular vcf snp interval written 9 weeks ago by taniamahmood380
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Comment: C: pileup to vcf
... Thanks a lot Jen, Galaxy team ...
written 9 weeks ago by taniamahmood380
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Answer: A: pileup to vcf
... Could you please tell me how you did it (made a vcf file from pilup dataset ) ? I am facing the same problem. ...
written 11 weeks ago by taniamahmood380
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Making dg SNP file-parameters setting complication for whole genome data
... I am stuck with setting parameters while making a dg SNP file for my whole genome data in tabular form. Could anyone please help me to set the parameters e.g. what to write in column with position box, Focus species box etc. Thanks!!! ...
snp written 3 months ago by taniamahmood380

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