User: marcoabbestia

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Posts by marcoabbestia

<prev • 11 results • page 1 of 2 • next >
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Comment: A: FREEC Your GC-content file is empty or is in a wrong format
... Thanks Kevin for your reply. I tried with a chromosome to test if it is work and now it is fine greetings Marco ...
written 2 days ago by marcoabbestia0
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FREEC Your GC-content file is empty or is in a wrong format
... Hi, I'd like to use FREEC without control to detect CNV in goat genome. I prepared my chromosome lenght file (goat_chr.len), my GC_content file, without mappability using bedtools on goat genome (example_GC_content.txt) and I prepared my config file: [general] chrLenFile = /illumina/runs/DNAPipeline ...
goat freec cnv written 2 days ago by marcoabbestia0
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Comment: C: Filtering Vcf File
... Hi, I have a mutect VCF file with the same FILTER column and PASS value I tried to run the vcffilter command but as you said it does not work. I saw that you solved the problem with grep. Please could you give me more information? Thanks ...
written 2.5 years ago by marcoabbestia0
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Comment: C: SNP calling from pool sequencing with freebayes
... Thank you, I saw the suggestions But I think that my problem is a little different. In that suggestion he wants to remove the SNP that are common in all 32 samples, I'm interested to remove the SNPs that are present in at least 2 of my 5 samples, for example  A B C 1 2 1 2 3 3  5 5 5  7 8 9  99 99 ...
written 3.3 years ago by marcoabbestia0
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SNP calling from pool sequencing with freebayes
... Hi all I have NGS data from 5 pools of 5 different breeds. My idea is to find a set of SNPs that identify each breed, then a SNP that is present only in one breed and not in the other four. I used several software and filters but when I visualize the results with IGV or Genome Browser the same SNP ...
ngs freebayes snp written 3.3 years ago by marcoabbestia0 • updated 26 days ago by Biostar ♦♦ 20
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Comment: C: filter several VCF files for fixed SNP
... Thank you very much. I tried with -c and the results do not change. I will try to create a single .vcf file and will use vcf-contrast. ...
written 3.3 years ago by marcoabbestia0
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Comment: C: filter several VCF files for fixed SNP
...   Thank you for the answer. I know that using pools of individuals we lost a lot of informations but as you have pointed out it was for economic reasons. I tried to apply very strong filter: Q>=100-DP>=100 as we are interested in very few SNP fixed (private allele) in each breed to traceabili ...
written 3.3 years ago by marcoabbestia0
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Comment: A: check duplicates in two columns
... thank you for the answers, my awk command is: awk -F'\t' 'NR==FNR{c[$1$2]++;next};c[$1$4] > 0' file.vcf file.map where $1$2 are #CHROM and POS in the .vcf file and $1$4 are #CHROM and POS for the .map file ...
written 3.3 years ago by marcoabbestia0 • updated 3.3 years ago by PoGibas4.7k
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check duplicates in two columns
... Hi all! I have two different files: a .map (from illumina genotyping with bead chip) and a .vcf (from NGS of a Pools of individuals). I'm interested in finding variations that are in both files, so I would have to compare for column 1: #CHROM and 4: POS (for .map) and column 1 #CHROM and 2: POS (fo ...
chip-seq snp sequencing written 3.3 years ago by marcoabbestia0
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Comment: A: filter several VCF files for fixed SNP
... Thank you for the answer. I know that using pools of individuals we lost a lot of informations but as you have pointed out it was for economic reasons. I tried to apply very strong filter: Q>=100-DP>=100 as we are interested in very few SNP fixed (private allele) in each breed to traceability ...
written 3.3 years ago by marcoabbestia0

Latest awards to marcoabbestia

Popular Question 11 months ago, created a question with more than 1,000 views. For filter several VCF files for fixed SNP
Popular Question 11 months ago, created a question with more than 1,000 views. For check duplicates in two columns
Popular Question 2.3 years ago, created a question with more than 1,000 views. For filter several VCF files for fixed SNP

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