User: Juliofdiaz

gravatar for Juliofdiaz
Juliofdiaz130
Reputation:
130
Status:
Trusted
Location:
Toronto, Ontario, Canada
Last seen:
7 months, 4 weeks ago
Joined:
7 years, 5 months ago
Email:
j*********@gmail.com

Posts by Juliofdiaz

<prev • 26 results • page 1 of 3 • next >
0
votes
0
answers
900
views
0
answers
How do I use haploid variant data to run finestructure or shapeit
... Hi, We are trying to use the [fineSTRUCTURE][1] software in order to identify haplotype information and to learn about the ancestry of 80 intraspecific bacteria. We have vcf files and bam files for each of the genomes of the 80 bacteria (We did whole genome sequencing and ref mapping to a complete g ...
shapeit bacteria haploid finestructure written 2.6 years ago by Juliofdiaz130
0
votes
0
answers
1.4k
views
0
answers
Retrieve Snps From Bacterial Whole Genome Msa For Ld Analysis
... I have whole bacterial genomes (very closely related) aligned and I would like to get the information of only the SNPs so that I can do some LD analysis. I would like to try to get them in the ped and map or plink formats preferably so that I can use them as imput for tassel. I haven't come across a ...
ld written 5.9 years ago by Juliofdiaz130
0
votes
1
answer
2.3k
views
1
answers
Comment: C: Varying Lengths In 2X150 Miseq Sequencing Data
... Thanks I meant ref mapping ...
written 6.3 years ago by Juliofdiaz130
2
votes
1
answer
2.3k
views
1
answer
Varying Lengths In 2X150 Miseq Sequencing Data
... I have data from a 2x150 Miseq run but I have noticed that the read lengths vary quite a lot. They range from 35 to 151 bp. I am interested in assembling these data with BWA or BOWTIE2 and I would like to know whether this is would be a problem and if not why? Thanks ...
illumina miseq written 6.3 years ago by Juliofdiaz130 • updated 6.3 years ago by Rahul Sharma600
0
votes
0
answers
1.7k
views
0
answers
Capture Jmol Measurements As Java Variables
... I came across some java code that implements jmol. However I am having a hard time learning how to capture the results of a measure command as a java variable instead of just having it printed in the console. This is the code import java.awt.BorderLayout; import java.awt.Container; import java.awt. ...
java written 6.4 years ago by Juliofdiaz130 • updated 3.2 years ago by Biostar ♦♦ 20
4
votes
1
answer
4.0k
views
1
answer
Filtering Vcf Variants Based On Sequencing Coverage
... Hello: I have produced a set of variants using the following pipeline ## SORT BAM FILE FROM REF MAPPING ## samtools sort r.bam" r_sorted" ## CREATE LIST OF POTENTIAL SNP OR INDEL ## samtools mpileup -uf ref.fa r_sorted.bam > r.bcf ## PARSE POTENTIAL SNP OR INDEL USING BAYESIAN INFERENCE ## bcfto ...
vcf samtools snp written 6.4 years ago by Juliofdiaz130 • updated 6.4 years ago by Ashutosh Pandey11k
1
vote
2
answers
1.6k
views
2
answers
Snp Quality Distribution Peaks At 222 From Variant Call Pile
... I have reference mapped paired end illumina reads and called variants using BWA and Samtools respectively. The resulting vcf was treated to remove high coverage SNPs with vcfutils.pl varFilter -D30, and then filtered for low quality SNPs using awk '($3=="*"&&$6>=50)||($3!="*"&&$6 ...
samtools bwa written 7.0 years ago by Juliofdiaz130 • updated 4.2 years ago by swbarnes26.0k
1
vote
2
answers
2.6k
views
2
answers
Comparing Quality Of Read 1 And Read2 Of Illumina Pe
... Hello: I have been asked to compare the quality of read one and read 2 of a illumina PE sequencing run and I am looking for the best way to represent it. I have come up with a couple of alternative: Count the number of bases under q 20 for each read and average it throughout the whole run, This me ...
illumina quality written 7.1 years ago by Juliofdiaz130 • updated 6.0 years ago by Biostar ♦♦ 20
0
votes
2
answers
8.4k
views
2
answers
Comment: C: Dp And Dp4 In Vcf
... At this point Im not too worried about calling low coverage regions because I will call those for each genome using GATK;s SNP calling guidelines. At this point I just want to call the SNPs that are highly reliable. You are right, using SNPs from the same genomes is not the best approach but the lac ...
written 7.1 years ago by Juliofdiaz130
0
votes
2
answers
8.4k
views
2
answers
Comment: C: Dp And Dp4 In Vcf
... I have about 30 genomes of the same strain so I will pool the high quality SNPS from those, and select only the ones that are present in all genomes. Besides I will include some of the known SNPs (kind of manually). This may introduce a small bias but to recalibrate the alignment quality scores it ...
written 7.1 years ago by Juliofdiaz130

Latest awards to Juliofdiaz

Great Question 8 months ago, created a question with more than 5,000 views. For Snp Depth From Vcf
Great Question 2.6 years ago, created a question with more than 5,000 views. For Dp And Dp4 In Vcf
Great Question 2.6 years ago, created a question with more than 5,000 views. For Bl2Seq In Blast+
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Capture Jmol Measurements As Java Variables
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Snp Quality Distribution Peaks At 222 From Variant Call Pile
Student 2.6 years ago, asked a question with at least 3 up-votes. For Reference Mapping To Consensus Fasta
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Capture Jmol Measurements As Java Variables
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Varying Lengths In 2X150 Miseq Sequencing Data
Great Question 3.2 years ago, created a question with more than 5,000 views. For Snp Depth From Vcf
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Samtools Depth And Gaps
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Samtools Depth And Gaps
Popular Question 5.9 years ago, created a question with more than 1,000 views. For Samtools Depth And Gaps
Popular Question 5.9 years ago, created a question with more than 1,000 views. For Bl2Seq In Blast+
Popular Question 5.9 years ago, created a question with more than 1,000 views. For Snp Depth From Vcf
Popular Question 5.9 years ago, created a question with more than 1,000 views. For Filtering Vcf Variants Based On Sequencing Coverage
Popular Question 7.1 years ago, created a question with more than 1,000 views. For Dp And Dp4 In Vcf
Popular Question 7.4 years ago, created a question with more than 1,000 views. For Snp Depth From Vcf
Popular Question 7.4 years ago, created a question with more than 1,000 views. For Bl2Seq In Blast+

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1447 users visited in the last hour