Forum: Bioinformatics
04-28-2015, 12:39 PM
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Replies: 5
Views: 2,108
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Forum: Bioinformatics
04-28-2015, 10:44 AM
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Replies: 5
Views: 2,108
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Forum: Bioinformatics
04-28-2015, 10:12 AM
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Replies: 5
Views: 2,108
Reference FASTA file for sequencing use
Hi all,
I downloaded FASTA files from NCBI and tried to use them in my sequencing pipeline. The issue is that within the FASTA file the sequences were represented using their genbank accession and...
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Forum: Bioinformatics
11-13-2012, 05:00 PM
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Replies: 1
Views: 1,726
Sample Exome FASTQ
Hi all
I was wondering if there are some exome analysis FASTQ files out there?
Any help will be highly appreciated.
Thanks.
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Forum: Bioinformatics
09-18-2012, 03:51 PM
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Replies: 1
Views: 1,603
Compile tabix
Hi all,
I downloaded the tabix source files from SourceForge but wasnt able to get it to compile under cygwin. does anyone how to start the compilation process under cygwin?
thanks.
a
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Forum: Bioinformatics
08-09-2012, 03:19 PM
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Replies: 0
Views: 926
Count of Variants
hi there,
does anyone know of a way to get count of SNP, indels, CNVs etc from a VCF file, so some thing like
SNPs = ?
Insertions = ?
Deletions = ?
CNVs = ?
thanks,
a
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Forum: Bioinformatics
08-07-2012, 04:30 PM
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Replies: 3
Views: 1,268
worked
hi there,
thank you, thats awesome, it worked.
In one of the columns the chromosomal location is mentioned as 1:1000 (for e.g.), can this script be slightly tweaked such that i can get a list...
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Forum: Bioinformatics
08-06-2012, 11:53 AM
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Replies: 3
Views: 1,268
Variant Effect Predictor Line Count
Hi all,
I am generating a VCF file and then running the Variant Effect Predictor (VEF) tool on it. This is in return giving me a new text file with the a list of variants and its potential effects....
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Forum: Bioinformatics
07-19-2012, 12:10 PM
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Replies: 4
Views: 3,940
Promoter or enhancer regions BED format
Hi all, One can download a BED file of human genome with exonic and intronic chromosomal coordinates.
I wanted to know if there is such a file for promoter or enhancer sites, best if it was in BED...
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Forum: Bioinformatics
07-19-2012, 12:05 PM
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Replies: 1
Views: 1,487
Homozygous Ref calls and no calls
Hi all, I was wondering if someone could help.
I am generating a vcf file based on the following command chain.
samtools sort eg2.bam eg2.sorted.bam samtools mpileup -uf referencegenomefile...
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Forum: Bioinformatics
07-11-2012, 03:35 PM
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Replies: 0
Views: 1,075
1000 Genomes individual genotype
I was wondering if someone could help.
When using the 1000Genomes browser I came across this statement “1000 Genomes individual genotypes display” on the search results page , if I understand...
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Forum: Bioinformatics
07-06-2012, 11:00 AM
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Replies: 0
Views: 727
all variant sites in the human genome
hi all,
i wanted to query for all sites in the human genome where variants occur. for e.g if we use dbSNP in vcf format one can run a bedIntersect on that.
is there any such file for the entire...
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Forum: Bioinformatics
07-06-2012, 10:58 AM
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Replies: 0
Views: 805
variant sites not listed in vcf
hi all
hope someone can help. The .vcf file generated after SNP calling contains variants with genotypes of 0/1 or 1/0 or 1/1.
does this mean that variants not detected in the vcf are homozygous...
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Forum: Bioinformatics
05-21-2012, 05:12 PM
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Replies: 0
Views: 909
dbSNP variants info
Hi all,
I have many, many dbSNP annotated SNPs (rs#) and for each one of them i want to get the chromosome number and location (HG19).
Is there any WEB API to get that information from a remote...
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Forum: Bioinformatics
05-17-2012, 10:57 AM
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Replies: 1
Views: 1,728
Issue with LiftOver
Hi all,
I have a lot if variants (more than 30K) with HG18 coordinates and i wanted HG19 coordinates for each one of them.
Aware that this can be done using liftover, the problem is i have to...
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Forum: Bioinformatics
04-25-2012, 01:59 PM
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Replies: 1
Views: 2,656
SAMTools and BED files
Hi there,
I am interested in looking at only certain SNP from the human genome and for each of them I have the chromosomal info and coordinate in both HG18 and HG19 systems.
When analyzing the...
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Forum: Bioinformatics
04-20-2012, 12:48 PM
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Replies: 0
Views: 954
1K Genomes mysql
Hi all,
I have been trying to access the public mysql instance of 1K genomes using the info provided here:
http://www.1000genomes.org/public-ensembl-mysql-instance
I am getting an error...
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Forum: Bioinformatics
04-16-2012, 03:58 PM
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Replies: 6
Views: 3,142
Update
Thanks, a lot, BLAST is working now. It had to do with the database being not available in the right format.
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Forum: Bioinformatics
04-16-2012, 03:06 PM
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Replies: 6
Views: 3,142
Files and still getting error
Right, so i used makeblastdb as follows
makeblastdb -in human_g1k_v37.fasta -title human_g1k_v37
it made three files each with
.psq, .phr and .pin file extensions
i am trying to execute...
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Forum: Bioinformatics
04-16-2012, 02:32 PM
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Replies: 6
Views: 3,142
Follow up info
Thanks for link to that article.
I am using blast-2.2.25+ on Ubuntu and formatdb -n human_g1k_v37_fasta.fasta
The exact error i get when i try to run blastn is index file not found for database...
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Forum: Bioinformatics
04-16-2012, 01:57 PM
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Replies: 6
Views: 3,142
FASTA database of human_g1k_v37.fasta
Hi all,
I want to BLAST using the human_g1k_v37_fasta as database. When i run formatdb on this file and run blast subsequent to that, i get a message stating index file not found.
Can someone...
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Forum: Bioinformatics
04-03-2012, 04:24 PM
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Replies: 2
Views: 2,107
Query Ensemble or USCS
Is there any automated way to get DNA sequences from UCSC genome browser or Ensemble for a list of chromosomal coordinates of interest.
I have several chromosomal coordinates sets and cannot do...
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Forum: Bioinformatics
03-28-2012, 02:54 PM
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Replies: 0
Views: 896
Find Variant in 1K Genomes
Hi there,
I am trying to determine the ref and alt allele used by 1K genomes at genomic loci. The VFC files, which contain the genotypes for all individual are available and when i search within...
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Forum: Bioinformatics
03-15-2012, 07:45 PM
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Replies: 0
Views: 1,338
Major Allele from FASTA file
Hi all,
I am working with the 1000 Genomes data and as a part of the analysis one has to input the reference genome file, this is provided by 1000 Genomes as a FASTA file.
When a .VCF file is...
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Forum: Bioinformatics
03-13-2012, 10:43 AM
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Replies: 11
Views: 3,523
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