User: tarek.mohamed
tarek.mohamed • 180
- Reputation:
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Posts by tarek.mohamed
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... Hi,
I am working with sequencing data generated by minion. I used minimap2 to align the long reads to reference human genome GRCh38. Now I want to call SNPs and indels, I have been searching for a tool that can work with bam files generated by minimap2.
1- Is there variant caller that work with fa ...
written 21 hours ago by
tarek.mohamed • 180
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Comment:
C: Long DNA reads aligned
... I am trying to call SNPs and indels, but all the tools I found are compatible with bam files generated with specific aligners.
Is there a universal SNP caller that an work with minimap2. I do not want to use nanopolish since it works only with fast5 files. I am currently testing nanosv, is there any ...
written 1 day ago by
tarek.mohamed • 180
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C: Long DNA reads aligned
... I used Minimap2 to align my minion reads to a reference genome. I then tried to sort it using picard but I got an error.
Why there is no sequence for this read?
$ java -jar /Users/tarekmagdyshehatamohamed/miniconda3/envs/bioinfo/share/picard-2.17.0-0/picard.jar SortSam I=BC01_minimap.sam O=BC01 ...
written 4 days ago by
tarek.mohamed • 180
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... Hi
What are the best long reads aligners?
I have dna sequencing data generated by minion. Which aligners should I use, I need to detect SNPs and indels downstream
Thanks
...
written 6 days ago by
tarek.mohamed • 180
• updated
6 days ago by
WouterDeCoster ♦ 30k
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... Thanks for the reply !
It was really helpful ...
written 23 days ago by
tarek.mohamed • 180
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... Hi,
Is there a way by which I can get the location of amino acids alteration for some snps
library(biomaRt)
ensembl<-useMart("ENSEMBL_MART_SNP")
ensembl<-useDataset("hsapiens_snp",mart=ensembl)
SN ...
written 23 days ago by
tarek.mohamed • 180
• updated
23 days ago by
b.nota ♦ 4.3k
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... Hi All,
I am using tximport to prepare quant.sf files generated from salmon for Deseq2 DEG analysis.
My quant.sf and txgenes files looks fine. However I got a message telling me that I have 3468transcripts missing from tx2gene.
I attached the code for tx2gene object generation.
What is causing this ...
written 11 weeks ago by
tarek.mohamed • 180
• updated
11 weeks ago by
h.mon ♦ 16k
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... Hi All ,
I did a LD analysis using a combination of bedtools, vcftools, and plink. I had 9000 SNPs distributed across 4 different genes which I did LD analysis for. Now I have LD analysis result (plink.ld) file. I
want to view the analysis graphically, which tool do you recommend?
[tmm447@qu ...
written 7 months ago by
tarek.mohamed • 180
• updated
7 months ago by
Hussain Ather • 880
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Comment:
C: linkage disequilibrium analysis
... Hi Kevin ,
I was able to do the analysis using a combination of bedtools, vcftools, and plink. I had 9000 SNPs distributed across 4 different genes which I did LD analysis for.
Now I have LD analysis result (plink.ld) file. I want to view the analysis graphically, which tool do you recommend?
...
written 7 months ago by
tarek.mohamed • 180
0
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769
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Comment:
C: linkage disequilibrium analysis
... Hi Kevin,
Thanks for your reply.
Actually, I tried vcftools, but I got negative values for r2 which of course does not make sense!
I am going try the long way approach, and I will let you know the updates.
Thanks,
T ...
written 8 months ago by
tarek.mohamed • 180
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For installation of package 'rmarkdown' had non-zero exit status
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