User: tarek.mohamed

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tarek.mohamed270
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Posts by tarek.mohamed

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Comment: C: impute2 output files to vcf
... I was able to get the genotypes as follows, re-ran impute2 with flag `-phase` to generate haplotypes file. Then I used shapeit to convert get vcf files shapeit -convert --input-haps impute2 --output-vcf impute2.vcf How can I keep the raw posterior-probability triplets in the .gen file ("GP")? ...
written 8 months ago by tarek.mohamed270
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Comment: C: impute2 output files to vcf
... I re-ran impute2 with flag `-phase` to generate haplotypes file. Then I used shapeit to convert get vcf files shapeit -convert --input-haps impute2 --output-vcf impute2.vcf ...
written 8 months ago by tarek.mohamed270
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Comment: C: impute2 output files to vcf
... How can I convert it using shapeit. I did not see that Gen format is an input option in shapeit convert? Thanks ...
written 8 months ago by tarek.mohamed270
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Comment: C: impute2 output files to vcf
... My impute2 file has a different identifier than what is required by bcftools to work (CHROM:POS_REF_ALT). ...
written 8 months ago by tarek.mohamed270
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impute2 output files to vcf
... Hi All, I need to know how can I deal with impute2 output file, how can I convert them to vcf files or is there a way by which I get vcf files as an impute2 output I has a vcf file with a gwas dataset for which I need to run impute2. I converted the vcf file into plink (bed,bim,fam) fromat, then ...
impute2 vcf file output written 8 months ago by tarek.mohamed270 • updated 8 months ago by RamRS28k
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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 14 months ago by tarek.mohamed270
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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 15 months ago by tarek.mohamed270 • updated 14 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 21 months ago by tarek.mohamed270 • updated 21 months ago by WouterDeCoster44k
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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 23 months ago by tarek.mohamed270
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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 23 months ago by tarek.mohamed270 • updated 23 months ago by WouterDeCoster44k

Latest awards to tarek.mohamed

Commentator 27 days ago, created a comment with at least 3 up-votes. For C: How is the design in DESeq2 work?
Great Question 5 months ago, created a question with more than 5,000 views. For installation of package 'rmarkdown' had non-zero exit status
Popular Question 5 months ago, created a question with more than 1,000 views. For Bowtie and % of RNA-Seq mappability.
Popular Question 7 months ago, created a question with more than 1,000 views. For Bowtie and % of RNA-Seq mappability.
Popular Question 7 months ago, created a question with more than 1,000 views. For qCount in QuasR for RNAseq quantification
Popular Question 11 months ago, created a question with more than 1,000 views. For Bowtie and % of RNA-Seq mappability.
Popular Question 11 months ago, created a question with more than 1,000 views. For qCount in QuasR for RNAseq quantification
Popular Question 14 months ago, created a question with more than 1,000 views. For Bowtie and % of RNA-Seq mappability.
Popular Question 14 months ago, created a question with more than 1,000 views. For qCount in QuasR for RNAseq quantification
Popular Question 14 months ago, created a question with more than 1,000 views. For study power / sample size estimation for GWAS
Popular Question 14 months ago, created a question with more than 1,000 views. For Bowtie and % of RNA-Seq mappability.
Popular Question 14 months ago, created a question with more than 1,000 views. For Bowtie and % of RNA-Seq mappability.
Popular Question 14 months ago, created a question with more than 1,000 views. For compare genotypes in two vcf files
Popular Question 14 months ago, created a question with more than 1,000 views. For compare genotypes in two vcf files
Popular Question 14 months ago, created a question with more than 1,000 views. For study power / sample size estimation for GWAS
Popular Question 14 months ago, created a question with more than 1,000 views. For can not install "ChIPpeakAnno"
Popular Question 14 months ago, created a question with more than 1,000 views. For Chip-seq data and Hi C data
Popular Question 17 months ago, created a question with more than 1,000 views. For study power / sample size estimation for GWAS
Good Answer 18 months ago, created an answer that was upvoted at least 5 times. For C: efetch error LWP::Protocol::https not installed
Popular Question 18 months ago, created a question with more than 1,000 views. For can not install "ChIPpeakAnno"
Appreciated 19 months ago, created a post with more than 5 votes. For C: efetch error LWP::Protocol::https not installed
Popular Question 19 months ago, created a question with more than 1,000 views. For can not install "ChIPpeakAnno"
Commentator 19 months ago, created a comment with at least 3 up-votes. For C: How is the design in DESeq2 work?
Popular Question 21 months ago, created a question with more than 1,000 views. For can not install "ChIPpeakAnno"
Popular Question 21 months ago, created a question with more than 1,000 views. For study power / sample size estimation for GWAS

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