User: Ana

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Ana70
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Posts by Ana

<prev • 60 results • page 1 of 6 • next >
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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 28 days ago by Ana70 • updated 28 days ago by h.mon11k
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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 28 days ago by Ana70
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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 28 days ago by Ana70
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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 29 days ago by Ana70
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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 4 weeks ago by Ana70
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Comment: C: finding candidate genes and their annotations
... I already know what are these candidate genes, I want to know their function! ...
written 5 weeks ago by Ana70
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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 5 weeks ago by Ana70
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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 8 weeks ago by Ana70
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Comment: C: Manhattan plot in r
... still does not work .... ...
written 4 months ago by Ana70
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Comment: C: how to adjust a Manhattan plot for bayes factor
... OK, I got the solution after reading "Manhattan" , I changed my code to this: > manhattan(chrom1,bp= "snp_pos", chr="chrom",p="env4_p",snp = "snp", logp = FALSE, ylim=c(-20,50)) The problem was logp, If TRUE, the -log10 of the p-value is plotted. It isn't very useful to plot raw p-valu ...
written 4 months ago by Ana70

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Supporter 28 days ago, voted at least 25 times.

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