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Search: Posts Made By: ashkot
Forum: Bioinformatics 04-28-2015, 12:39 PM
Replies: 5
Views: 2,108
Posted By ashkot
We did take those file and there is no issue with...

We did take those file and there is no issue with those files. There are some other old genomes which we require and that is the issue.

I am wondering if there is some code that can standardize...
Forum: Bioinformatics 04-28-2015, 10:44 AM
Replies: 5
Views: 2,108
Posted By ashkot
That site has only up to hg18 for human but if I...

That site has only up to hg18 for human but if I wanted to use much older genome assemblies? And my work is for human genome analysis.
Forum: Bioinformatics 04-28-2015, 10:12 AM
Replies: 5
Views: 2,108
Posted By ashkot
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...
Forum: Bioinformatics 11-13-2012, 05:00 PM
Replies: 1
Views: 1,726
Posted By ashkot
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.
Forum: Bioinformatics 09-18-2012, 03:51 PM
Replies: 1
Views: 1,603
Posted By ashkot
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
Forum: Bioinformatics 08-09-2012, 03:19 PM
Replies: 0
Views: 926
Posted By ashkot
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
Forum: Bioinformatics 08-07-2012, 04:30 PM
Replies: 3
Views: 1,268
Posted By ashkot
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...
Forum: Bioinformatics 08-06-2012, 11:53 AM
Replies: 3
Views: 1,268
Posted By ashkot
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....
Forum: Bioinformatics 07-19-2012, 12:10 PM
Replies: 4
Views: 3,940
Posted By ashkot
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...
Forum: Bioinformatics 07-19-2012, 12:05 PM
Replies: 1
Views: 1,487
Posted By ashkot
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...
Forum: Bioinformatics 07-11-2012, 03:35 PM
Replies: 0
Views: 1,075
Posted By ashkot
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...
Forum: Bioinformatics 07-06-2012, 11:00 AM
Replies: 0
Views: 727
Posted By ashkot
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...
Forum: Bioinformatics 07-06-2012, 10:58 AM
Replies: 0
Views: 805
Posted By ashkot
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...
Forum: Bioinformatics 05-21-2012, 05:12 PM
Replies: 0
Views: 909
Posted By ashkot
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...
Forum: Bioinformatics 05-17-2012, 10:57 AM
Replies: 1
Views: 1,728
Posted By ashkot
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...
Forum: Bioinformatics 04-25-2012, 01:59 PM
Replies: 1
Views: 2,656
Posted By ashkot
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...
Forum: Bioinformatics 04-20-2012, 12:48 PM
Replies: 0
Views: 954
Posted By ashkot
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...
Forum: Bioinformatics 04-16-2012, 03:58 PM
Replies: 6
Views: 3,142
Posted By ashkot
Update

Thanks, a lot, BLAST is working now. It had to do with the database being not available in the right format.
Forum: Bioinformatics 04-16-2012, 03:06 PM
Replies: 6
Views: 3,142
Posted By ashkot
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...
Forum: Bioinformatics 04-16-2012, 02:32 PM
Replies: 6
Views: 3,142
Posted By ashkot
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...
Forum: Bioinformatics 04-16-2012, 01:57 PM
Replies: 6
Views: 3,142
Posted By ashkot
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...
Forum: Bioinformatics 04-03-2012, 04:24 PM
Replies: 2
Views: 2,107
Posted By ashkot
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...
Forum: Bioinformatics 03-28-2012, 02:54 PM
Replies: 0
Views: 896
Posted By ashkot
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...
Forum: Bioinformatics 03-15-2012, 07:45 PM
Replies: 0
Views: 1,338
Posted By ashkot
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...
Forum: Bioinformatics 03-13-2012, 10:43 AM
Replies: 11
Views: 3,523
Posted By ashkot
jflowers, i did exactly as you suggested and the...

jflowers, i did exactly as you suggested and the program output a huge VCF file although there is not a single 0/0 row. I am not sure what could be going on here?

Any further ideas?

Thanks.
Showing results 1 to 25 of 59

 


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