User: Ana

gravatar for Ana
Ana90
Reputation:
90
Status:
Trusted
Location:
Last seen:
1 week ago
Joined:
1 year, 2 months ago
Email:
**********@gmail.com

Posts by Ana

<prev • 61 results • page 1 of 7 • next >
0
votes
0
answers
55
views
0
answers
estimate population allele frequencies with EM (expectation-maximation) algorithm using R
... Hello everyone, I have asked this question in Stack Exchange Bioinformatics forum, unfortunately I have not been able to get any help there. So, I am asking it here, maybe some R professionalists can help me to fix the final part of my R-code. I would really appreciate if anyone can help me to resol ...
R em algorithm written 12 days ago by Ana90
2
votes
2
answers
194
views
5 follow
2
answers
how to handle reads that mapped to multiple genes
... Hello every one, this is a question related to my [previous question][1] that I posted. I have aligned a bunch of whole genome shot reads against Pangenome proteins by using DIAMOND protein aligner. After filtering for e-value, identity percentage and bit score, I still get some reads which perfectl ...
alignment whole genome sequencing written 12 weeks ago by Ana90 • updated 12 weeks ago by h.mon13k
0
votes
0
answers
257
views
0
answers
Comment: C: multiple DNA reads aligned to the same gene
... Thanks @genomax, very helpful. Then my last question is that if the same read matches to multiple genes then can I say all these genes present in my DNA sequence data-set? Because the final aim of doing this alignment is to understand which gene is present and which gene is absent in my DNA sequence ...
written 12 weeks ago by Ana90
0
votes
0
answers
257
views
0
answers
Comment: C: multiple DNA sequences aligned to the same gene
... Thanks a lot Asaf, got it now. Another little question, how about if the same read matches to multiple genes? like this: could it be possible? HWI-ST913:300:C5W5DACXX:7:1101:1649:2180 Ha12_00033467 100.0 33 0 0 100 2 91 123 7.8e-12 65.9 HWI-ST913:300:C5W5DACXX:7:1101:1649:2180 Ha10_0000053 ...
written 12 weeks ago by Ana90
4
votes
0
answers
257
views
5 follow
0
answers
multiple DNA reads aligned to the same gene
... Hello everyone, I have aligned a bunch of whole genome shotgun sequencing data against Pangenome protein sequences by using DIAMOND protein aligner to find out which genes are present and which are absent in my DNA sequence data . I am sorry if my question is dumb, but I am new in alignment and lea ...
protein alignment whole genome written 12 weeks ago by Ana90
0
votes
0
answers
257
views
0
answers
Comment: C: Software to analyze Diamond data
... Hey, guys. I am having the same issue. I have aligned a set of shotgun sequencing data against nearly 600 genes using DIAMOND blastx. I want to know which genes are present and which are absent in my shotgun sequencing data! Do you have any recommendation how can I do it? ...
written 12 weeks ago by Ana90
0
votes
2
answers
265
views
2
answers
Comment: C: finding candidate genes and their annotations
... I already know what are these candidate genes, I want to know their function! ...
written 3 months ago by Ana90
1
vote
2
answers
265
views
6 follow
2
answers
finding function of genes from their coordinates
... Hi everyone, I made some Manhattan plots and I can see some very tall peaks on chromosome 6 and 12. I already have the coordinates of the gens (chromosome, starting and ending positions), I want to know the function. I am new in this and does anyone have any idea where should I start? ...
gene annotation written 3 months ago by Ana90
1
vote
0
answers
211
views
0
answers
LD between CNVs and exterior SNPs
... Hello everyone, I have a few copy number variants (all multi-allelic) and trying to estimate LD between these CNVs and all SNPs across the genome (I am interested in LD between CNVs and "exterior" SNPs). In the past I have estimated LD between biallelic SNPs. I just converted my vcf file into 0,1,2 ...
snp cnv ld written 3 months ago by Ana90
0
votes
1
answer
88
views
1
answers
Comment: C: Manhattan plot in r
... still does not work .... ...
written 5 months ago by Ana90

Latest awards to Ana

Supporter 12 weeks ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1045 users visited in the last hour