User: deepti1rao

gravatar for deepti1rao
deepti1rao30
Reputation:
30
Status:
New User
Location:
Last seen:
3 weeks, 5 days ago
Joined:
2 years, 9 months ago
Email:
d*********@gmail.com

Posts by deepti1rao

<prev • 82 results • page 1 of 9 • next >
0
votes
0
answers
100
views
0
answers
Assembly size decreased after using SSPACE for scaffolding
... I had 57,206 contigs from the Velvet assembler, with an N50 of 15,957. I got an assembly size of 348,942,280 bp (without any Ns). When I fed these contigs into SSPACE, the N50 improved to 30,443, but my assembly size **decreased** to 348,541,909 bp, despite the inclusion of 31,358 Ns. I used the s ...
sspace contigs assembly size scaffolding written 26 days ago by deepti1rao30 • updated 12 days ago by Biostar ♦♦ 20
0
votes
0
answers
395
views
0
answers
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 16 months ago by deepti1rao30
0
votes
0
answers
395
views
0
answers
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 16 months ago by deepti1rao30
0
votes
1
answer
1.3k
views
1
answers
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 16 months ago by deepti1rao30
0
votes
0
answers
395
views
0
answers
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 16 months ago by deepti1rao30
1
vote
3
answers
575
views
3
answers
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 16 months ago by deepti1rao30 • updated 15 months ago by jean.elbers1.3k
0
votes
0
answers
395
views
0
answers
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 16 months ago by deepti1rao30
0
votes
0
answers
377
views
0
answers
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 18 months ago by deepti1rao30
0
votes
1
answer
1.4k
views
1
answers
Comment: C: Need help with R script to edit x-axis of snp density plot
... Can anyone help with this? ...
written 18 months ago by deepti1rao30
5
votes
1
answer
1.4k
views
6 follow
1
answer
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 19 months ago by deepti1rao30 • updated 16 months ago by bernatgel2.4k

Latest awards to deepti1rao

Popular Question 16 months ago, created a question with more than 1,000 views. For Is indel realigning necessary for INDEL discovery?
Popular Question 16 months ago, created a question with more than 1,000 views. For Reference based assembly with multiple references
Popular Question 16 months ago, created a question with more than 1,000 views. For Trimming reads with prinseq
Popular Question 16 months ago, created a question with more than 1,000 views. For Removal of PCR dupliactes from trimmed reads
Popular Question 16 months ago, created a question with more than 1,000 views. For Minimum length of reads
Popular Question 16 months ago, created a question with more than 1,000 views. For Need help with R script to edit x-axis of snp density plot

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 745 users visited in the last hour