User: tarek.mohamed

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tarek.mohamed250
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Posts by tarek.mohamed

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Comment: C: Minion reads error rate for indels and snps
... Hi, I have the vcf file, but I wonder how can I do the actual error rate analysis? Thanks ...
written 6 months ago by tarek.mohamed250
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Minion reads error rate for indels and snps
... Dear All, How can I analyze the error rate of my Minion reads? how to calculate the error rate of insertion, deletion and Substitutions? thankT ...
rate minion error written 6 months ago by tarek.mohamed250 • updated 5 months ago by Biostar ♦♦ 20
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structural variant vcf file comparison
... Hi, I have six vcf files (cases vs control) that contain structural variants with variable length from nanopore sequence run. These vcf files were generated using NGMLR aligner followed by sniffle. What is the best way/tool to compare these files? Thanks Tarek ...
vcf sv written 12 months ago by tarek.mohamed250 • updated 12 months ago by WouterDeCoster42k
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Comment: C: Using one bam file with huge coverage, How to generate several bam files with di
... Thanks for the reply! This command will exclude 90% of reads at a position. Which reads will be excluded, is it a random process? Do I have any power to select on what bases these reads will be excluded? as for example keep the reads with highest mapping quality or base quality scores? Since the c ...
written 14 months ago by tarek.mohamed250
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Using one bam file with huge coverage, How to generate several bam files with different coverage
... Hi, I have a bam file includes a single gene sequence with huge coverage (> 5000X) from which I want to call snps. I have several snps previously identified in my sample which I am going to use as control to test my pipeline. From my original bam file , I want to generate some bam files with dif ...
filter snps caller bam written 14 months ago by tarek.mohamed250 • updated 14 months ago by WouterDeCoster42k
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Comment: C: bcftools mpileup output format
... Hi Thanks for the reply I know about bcftools call, but I want to understand all of mpileup output because as you mentioned this will be used by bcftools call. By modifying bcftools mpileup parameters, hopefully I can call variants form the long reads sequence I have. My bam file pile (with huge de ...
written 14 months ago by tarek.mohamed250
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bcftools mpileup output format
... Hi All, I am trying to use modify bcftools mpileup / call to detect snps from nanopore sequence data with huger depth ( >5000X). I need to understand the format of the mpileup shown bellow. I used position 84303804 as an example > bcftools mpileup --skip-indels -C 0 -d 250 -r chr9:8427 ...
bcftools mpileup written 14 months ago by tarek.mohamed250
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Percent identity plot
... Dear All What are the available tools for plotting sequence reads percent identitiy over a certain genetic locus in multiple samples. I have Sam/bam files for some samples and I want to compare and plot percent identity for one gene across all samples ...
alignment identitiy precent plot written 15 months ago by tarek.mohamed250 • updated 15 months ago by h.mon28k
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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 16 months ago by tarek.mohamed250 • updated 12 months ago by WouterDeCoster42k
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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 16 months ago by tarek.mohamed250

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Popular Question 5 months ago, created a question with more than 1,000 views. For Bowtie and % of RNA-Seq mappability.
Popular Question 5 months ago, created a question with more than 1,000 views. For qCount in QuasR for RNAseq quantification
Popular Question 5 months ago, created a question with more than 1,000 views. For study power / sample size estimation for GWAS
Popular Question 5 months ago, created a question with more than 1,000 views. For Bowtie and % of RNA-Seq mappability.
Popular Question 5 months ago, created a question with more than 1,000 views. For Bowtie and % of RNA-Seq mappability.
Popular Question 5 months ago, created a question with more than 1,000 views. For compare genotypes in two vcf files
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Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For C: efetch error LWP::Protocol::https not installed
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