User: F

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F3.2k
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I am learning everyday

Posts by F

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Comment: C: dNdScv error: Zero coding substitutions found in this dataset
... Sorry, I likely analyzed my data with dNdScv successfully; However, I am not sure how I could achieve three ouputs 1- For getting the percentage of driver mutations in each gene and in different mutation classes I am not sure which table gives me these. For example > print(head(sel_cv), d ...
written 13 hours ago by F3.2k
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Comment: C: VCF file filtration
... You are most welcome, best of luck ...
written 1 day ago by F3.2k
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Comment: C: VCF file filtration
... Sorry I am not sure, I have started whole genome sequencing since 2 weeks ago. But, I found a tool named MAFtools in R very helpful although I have not used that yet. ...
written 1 day ago by F3.2k
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Comment: C: VCF file filtration
... I would upload my .vcf files in galaxy and using bcftools I would filterate my files. For example in galaxy the default for DP is 10 and you can change that. ...
written 1 day ago by F3.2k
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Comment: C: VEP vs webserver Polyphen scores
... Sorry, I have uploaded my separate SNV and indel as vcf in Vep. I want to score the functional impact of each missense non-synonomous mutation (from 0, non-impactful to 1 highly impactful), synonymous mutation a score of 0 impact and truncating mutations (Non-sense and frameshift mutations) a score ...
written 2 days ago by F3.2k
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Comment: C: Converting a VCF with SNPs and indels to BED format
... Sorry I don't know I got error [fi1d18@cyan01 ~]$ module load bedtools/2.21.0 [fi1d18@cyan01 ~]$ $ cut -f1-5 foo_snvs.bed | awk -v FS="\t" -v OFS="\t" '{ print $1, $2, $3, $4, $5, "+"; }' > foo_snvs.bed6 bash: $: command not found [fi1d18@cyan01 ~]$ ...
written 3 days ago by F3.2k
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Comment: C: dNdScv error: Zero coding substitutions found in this dataset
... Thanks a lot, very very appreciated as I was struggling especially about the filtration based on influencing proteins. My project is `responding or non-responding to chemotherapy in oesophagus adenocarcinoma`; So, we have whole genome sequencing of responder patients (tumour vs normal tissue) and ...
written 3 days ago by F3.2k
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Comment: C: Converting a VCF with SNPs and indels to BED format
... Sorry, I have some .vcf files contain only snp (I guess because I have separate vcf files for somatic indels and structural variants) I used this command to convert vcf to bed vcf2bed --snvs < foo.vcf > foo_snvs.bed My bed does not have any column named strand How I can extract the st ...
written 3 days ago by F3.2k
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Comment: C: dNdScv error: Zero coding substitutions found in this dataset
... Sorry, For getting better results, do you suggest me to use original vcf files as input for your software or I should first filtrate vcf file for minor allele frequency and variant with deleterious impact of the protein? ...
written 3 days ago by F3.2k
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Comment: C: VEP vs webserver Polyphen scores
... Sorry, I have uploaded a vcf file contains snp in Vep but I am not able to find reference allele when I am downloading results as txt http://grch37.ensembl.org/Homo_sapiens/Tools/VEP/Ticket?tl=oICvFAZfvx7Og6CX Could you please have a look because I need both reference and variant allele Thank y ...
written 4 days ago by F3.2k

Latest awards to F

Popular Question 6 days ago, created a question with more than 1,000 views. For UCSC_TFBS option in DAVID
Great Question 8 days ago, created a question with more than 5,000 views. For R - removing column names from matrix
Popular Question 14 days ago, created a question with more than 1,000 views. For UCSC_TFBS option in DAVID
Great Question 15 days ago, created a question with more than 5,000 views. For R - removing column names from matrix
Popular Question 17 days ago, created a question with more than 1,000 views. For UCSC_TFBS option in DAVID
Popular Question 17 days ago, created a question with more than 1,000 views. For UCSC_TFBS option in DAVID
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Popular Question 3 months ago, created a question with more than 1,000 views. For only a few differential expressed genes

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