User: Fid_o

gravatar for Fid_o
Fid_o20
Reputation:
20
Status:
New User
Location:
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 >
0
votes
0
answers
112
views
0
answers
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_o20
0
votes
0
answers
158
views
0
answers
Comment: C: SNP Calling using Genome Analysis Toolkit
... Thanks Pierre, would you advise what newer pipeline there is? ...
written 10 weeks ago by Fid_o20
0
votes
0
answers
158
views
0
answers
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_o20
0
votes
0
answers
158
views
0
answers
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_o20
0
votes
0
answers
202
views
0
answers
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_o20 • updated 7 months ago by Biostar ♦♦ 20
0
votes
0
answers
426
views
0
answers
Comment: C: Quality check of sequences in fasta format
... Thank you for that help and insight. Absolutely helpful. ...
written 9 months ago by Fid_o20
0
votes
0
answers
426
views
0
answers
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_o20
0
votes
0
answers
426
views
0
answers
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_o20
0
votes
0
answers
426
views
0
answers
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_o20
2
votes
0
answers
426
views
0
answers
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_o20 • updated 9 months ago by GenoMax94k

Latest awards to Fid_o

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

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2295 users visited in the last hour