User: tarek.mohamed

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tarek.mohamed180
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Posts by tarek.mohamed

<prev • 86 results • page 1 of 9 • next >
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Nanopore SNP and indels calling tool
... 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 ...
snps indels tools calling nanopore written 21 hours ago by tarek.mohamed180
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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.mohamed180
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Comment: 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.mohamed180
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Long DNA reads aligned
... 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 ...
nanopore written 6 days ago by tarek.mohamed180 • updated 6 days ago by WouterDeCoster30k
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Comment: C: amino acid alteration position for SNPs using biomart
... Thanks for the reply ! It was really helpful ...
written 23 days ago by tarek.mohamed180
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amino acid alteration position for SNPs using biomart
... 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 ...
snps locations biomart aminoacids written 23 days ago by tarek.mohamed180 • updated 23 days ago by b.nota4.3k
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using tximport to prepare salmon quantification files for DEG analysis
... 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 ...
tximport rna-seq written 11 weeks ago by tarek.mohamed180 • updated 11 weeks ago by h.mon16k
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Plotting linkage equilibrium results
... 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 ...
plotting ld heatmap linkage disequilibrium plink written 7 months ago by tarek.mohamed180 • updated 7 months ago by Hussain Ather880
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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.mohamed180
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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.mohamed180

Latest awards to tarek.mohamed

Popular Question 6 weeks ago, created a question with more than 1,000 views. For study power / sample size estimation for GWAS
Popular Question 11 weeks ago, created a question with more than 1,000 views. For study power / sample size estimation for GWAS
Scholar 7 months ago, created an answer that has been accepted. For A: Converting numeric to alphanumeric allele codes
Teacher 7 months ago, created an answer with at least 3 up-votes. For C: efetch error LWP::Protocol::https not installed
Scholar 9 months ago, created an answer that has been accepted. For A: Converting numeric to alphanumeric allele codes
Popular Question 21 months ago, created a question with more than 1,000 views. For installation of package 'rmarkdown' had non-zero exit status

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