User: deepti1rao

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deepti1rao30
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Posts by deepti1rao

<prev • 81 results • page 1 of 9 • next >
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Comment: C: Should I replace heterozygous variants to make a consensus
... Currently, I do not have enough data to take up a proper assembly. I have tried velvet de novo. When I mapped the resulting contigs to the reference, I found a lot of misassemblies and the coverage is far less than what my reads cover. I think all the reference based assemblers initially do a de n ...
written 13 months ago by deepti1rao30
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Comment: C: Should I replace heterozygous variants to make a consensus
... Thanks for this idea! Are two base codes understood and accepted by tools like Bowtie2, samtools etc for future analyses?? ...
written 13 months ago by deepti1rao30
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Comment: C: IUAPC codes in consensus sequence ? samtools mpileup / bcftools call / bcftools
... Did you find a solution to this? Please share if you did. ...
written 13 months ago by deepti1rao30
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Comment: C: Should I replace heterozygous variants to make a consensus
... Hi! The goal is to do a reference based assembly. 97% of our reads align to the reference. ...
written 13 months ago by deepti1rao30
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Reference based assembly
... I'm trying to do a reference-aided assembly of a new variety of rice genome. I have mapped my Illumina reads to the reference and replaced the uncovered bases with Ns. I have now used this masked genome fasta file as a reference to map my reads once again. I wish to pull out the variants by doing so ...
assembly reference written 13 months ago by deepti1rao30 • updated 12 months ago by jean.elbers1.3k
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Should I replace heterozygous variants to make a consensus
... I want to make a consensus genome by replacing variants. I want to replace homozygous variants in the reference. Is it right to replace the heterozygous variants? The ALT allele must correspond to the homozygous chromosome of a diploid organism. That's my understanding. So I am thinking of not repla ...
consensus genome heterozygous variant assembly written 13 months ago by deepti1rao30
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vcf v4.2 consequences of missense snps
... It appears that SIFT cannot deal with vcf version 4.2 files. I am dealing with a plant genome. What other options (tools) do I have for finding the consequences of missense snps? ...
vcf plant snps missense sift written 15 months ago by deepti1rao30
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Comment: C: Need help with R script to edit x-axis of snp density plot
... Can anyone help with this? ...
written 15 months ago by deepti1rao30
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Need help with R script to edit x-axis of snp density plot
... I am using the following code to plot Chromosome-wide SNP densities. It generates the attached output, such that X-axis for all the chromosomes is of the same length. It can be misleading, as it appears as if the right ends of some (reads short) chromosomes is totally devoid of snps. Can I have shor ...
R snps density chromosome written 16 months ago by deepti1rao30 • updated 13 months ago by bernatgel2.2k
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Comment: C: Known SNPs for rice for Base recalibration using GATK
... This link does not contain anything. ftp://ftp.ncbi.nih.gov/snp/organisms/rice_4530/VCF/ Where can I find known rice snps (indica and japonica, both) ...
written 16 months ago by deepti1rao30

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