User: tarek.mohamed

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tarek.mohamed180
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Posts by tarek.mohamed

<prev • 91 results • page 1 of 10 • next >
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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 days ago by tarek.mohamed180
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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 15 days ago by tarek.mohamed180 • updated 15 days ago by WouterDeCoster32k
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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 20 days ago by tarek.mohamed180
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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 20 days ago by tarek.mohamed180
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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 6 weeks ago by tarek.mohamed180 • updated 6 weeks ago by h.mon19k
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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 8 weeks 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 8 weeks 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 8 weeks 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 9 weeks ago by tarek.mohamed180 • updated 9 weeks ago by WouterDeCoster32k
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Comment: C: amino acid alteration position for SNPs using biomart
... Thanks for the reply ! It was really helpful ...
written 11 weeks ago by tarek.mohamed180

Latest awards to tarek.mohamed

Popular Question 3 months ago, created a question with more than 1,000 views. For study power / sample size estimation for GWAS
Popular Question 4 months ago, created a question with more than 1,000 views. For study power / sample size estimation for GWAS
Scholar 9 months ago, created an answer that has been accepted. For A: Converting numeric to alphanumeric allele codes
Teacher 9 months ago, created an answer with at least 3 up-votes. For C: efetch error LWP::Protocol::https not installed
Scholar 11 months ago, created an answer that has been accepted. For A: Converting numeric to alphanumeric allele codes
Popular Question 23 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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