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User: Fid_o

gravatar for Fid_o
Fid_o • 20
Reputation:
20
Status:
New User
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Last seen:
3 weeks, 4 days ago
Joined:
1 year, 8 months ago
Email:
s***********@gmail.com

I am a Bioinformatics student, quite new in the field.

Posts by Fid_o

<prev • 25 results • page 1 of 3 • next >
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Tool to annotate VCF File from bacterial genome SNPs
... Hello, I am working on hundreds of bacterial sequences and I am analysing single nucleotide polymorphisms (SNPs). I have a VCF file which I extracted using snp-sites. I would like to annotate my variants (SNPs) with their biological phenotypes. Is there any good tool I would use to do this? Reg ...
genome gene snp sequencing written 6 weeks ago by Fid_o • 20
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Comment: C: SNP Calling using Genome Analysis Toolkit
... Thanks Pierre, would you advise what newer pipeline there is? ...
written 10 weeks ago by Fid_o • 20
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Comment: C: SNP Calling using Genome Analysis Toolkit
... Yes, absolutely that - tally the differences. That is what I want to do - multiple alignments and phylogenetic tree construction ...
written 10 weeks ago by Fid_o • 20
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SNP Calling using Genome Analysis Toolkit
... Greetings, I want to do SNP analysis (variant call) using the steps below which I got from https://approachedinthelimit.wordpress.com/2015/10/09/variant-calling-with-gatk/ These steps use short reads. But I am working on assembled whole genome bacterial sequences, how do I go about it using asse ...
genome assembly alignment snp sequencing written 10 weeks ago by Fid_o • 20
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Extracting lineages from phylogenetic trees
... Greetings, Is there a way to extract evolutionary lineages from phylogenetic trees? I am working on 465 bacterial sequences. The bacteria I am working with has known Lineage 1 and Lineage 2. I am examining the emergence of a newer lineage, which I will call 2.1. I do not know how many of the seque ...
lineage phylogenetics alignment written 9 months ago by Fid_o • 20 • updated 7 months ago by Biostar ♦♦ 20
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Comment: C: Quality check of sequences in fasta format
... Thank you for that help and insight. Absolutely helpful. ...
written 9 months ago by Fid_o • 20
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Comment: C: Quality check of sequences in fasta format
... @genomax. Thank you for your replies. I needed quality check for my SNP analysis on these sequences. ...
written 9 months ago by Fid_o • 20
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Comment: C: Quality check of sequences in fasta format
... @genomax I don't have the fasta/qual files, it's just the fasta files. This being the case, can I safely convert fasta files to fastq for purpose of FASTQC use? My first reservations with conversion would be possibility of introducing errors to the files. ...
written 9 months ago by Fid_o • 20
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Comment: C: Quality check of sequences in fasta format
... @genomax, I mean to check the quality like we would check using FASTQC. I realise FASTQC takes in Fastq files, I have .FASTA files. ...
written 9 months ago by Fid_o • 20
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Quality check of sequences in fasta format
... Hello, I have .FASTA files of bacterial genomes. I want to check quality of the sequences. Which program accepts quality analysis of .FASTA files? Cheers! ...
genome assembly alignment written 9 months ago by Fid_o • 20 • updated 9 months ago by GenoMax ♦ 94k

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Popular Question 6 weeks ago, created a question with more than 1,000 views. For Python Script to map reads to reference sequence
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