User: Juliofdiaz

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Juliofdiaz130
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130
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Toronto, Ontario, Canada
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1 month, 3 weeks ago
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8 years, 7 months ago
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Posts by Juliofdiaz

<prev • 29 results • page 1 of 3 • next >
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Comment: C: Parsing GFF with biopython throws error
... When I try your code I get a different exception: Traceback (most recent call last): File "test2.py", line 13, in for x in GFF.parse( open( t.name ) ): File "/home/zoo/user/anaconda2/lib/python3.7/site-packages/BCBio/GFF/GFFParser.py", line 746, in parse target_line ...
written 10 weeks ago by Juliofdiaz130
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Comment: C: Parsing GFF with biopython throws error
... Thanks, fixed it in the post ...
written 10 weeks ago by Juliofdiaz130
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Parsing GFF with biopython throws error
... I using bio python to parse a GFF file, and I am using some of the sample code I found in their [website][1] (Basic GFF parsing section). from BCBio import GFF in_file = "my_genome.gff" in_handle = open(in_file) for rec in GFF.parse(in_handle): print(rec) in_ha ...
gff biopython written 10 weeks ago by Juliofdiaz130 • updated 6 weeks ago by Biostar ♦♦ 20
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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 3.8 years ago by Juliofdiaz130
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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 7.1 years ago by Juliofdiaz130
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Comment: C: Varying Lengths In 2X150 Miseq Sequencing Data
... Thanks I meant ref mapping ...
written 7.5 years ago by Juliofdiaz130
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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 7.5 years ago by Juliofdiaz130 • updated 7.5 years ago by Rahul Sharma600
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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 7.6 years ago by Juliofdiaz130 • updated 4.4 years ago by Biostar ♦♦ 20
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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 7.6 years ago by Juliofdiaz130 • updated 7.6 years ago by Ashutosh Pandey12k
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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 8.2 years ago by Juliofdiaz130 • updated 5.4 years ago by swbarnes28.6k

Latest awards to Juliofdiaz

Epic Question 22 months ago, created a question with more than 10,000 views. For Snp Depth From Vcf
Popular Question 22 months ago, created a question with more than 1,000 views. For Capture Jmol Measurements As Java Variables
Great Question 22 months ago, created a question with more than 5,000 views. For Snp Depth From Vcf
Great Question 3.8 years ago, created a question with more than 5,000 views. For Dp And Dp4 In Vcf
Great Question 3.8 years ago, created a question with more than 5,000 views. For Bl2Seq In Blast+
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Capture Jmol Measurements As Java Variables
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Snp Quality Distribution Peaks At 222 From Variant Call Pile
Student 3.8 years ago, asked a question with at least 3 up-votes. For Reference Mapping To Consensus Fasta
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Capture Jmol Measurements As Java Variables
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Varying Lengths In 2X150 Miseq Sequencing Data
Great Question 4.4 years ago, created a question with more than 5,000 views. For Snp Depth From Vcf
Popular Question 4.6 years ago, created a question with more than 1,000 views. For Samtools Depth And Gaps
Popular Question 5.4 years ago, created a question with more than 1,000 views. For Samtools Depth And Gaps
Popular Question 7.1 years ago, created a question with more than 1,000 views. For Bl2Seq In Blast+
Popular Question 7.1 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 Snp Depth From Vcf
Popular Question 7.1 years ago, created a question with more than 1,000 views. For Samtools Depth And Gaps
Popular Question 8.3 years ago, created a question with more than 1,000 views. For Dp And Dp4 In Vcf
Popular Question 8.6 years ago, created a question with more than 1,000 views. For Snp Depth From Vcf
Popular Question 8.6 years ago, created a question with more than 1,000 views. For Bl2Seq In Blast+

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