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Forum: Bioinformatics 03-22-2012, 09:51 AM
Replies: 0
Views: 1,050
Posted By rudi283
SNPs(135) gtf file from UCSC

Hi,

I downloaded gtf files from UCSC for all SNPs(135) each chromosome separate. When I annotated it onto my refseq I realized that quite often I see more that one rs number for same position on a...
Forum: Sample Prep / Library Generation 11-30-2011, 02:23 AM
Replies: 12
Views: 11,975
Posted By rudi283
I always use Qubit to quantify the input DNA,...

I always use Qubit to quantify the input DNA, nanodrop only to check the quality

before the capture/sequencing I check the samples on qubit and bioanalyzer
Forum: Bioinformatics 11-30-2011, 02:13 AM
Replies: 4
Views: 1,961
Posted By rudi283
In Genomics Workbench, from CLC Bio, you can...

In Genomics Workbench, from CLC Bio, you can remove PCR duplicates before alignment
Forum: Bioinformatics 10-21-2011, 05:58 AM
Replies: 2
Views: 1,218
Posted By rudi283
Thank you very much! I'll definitely have a go,...

Thank you very much!
I'll definitely have a go, when the ensembl will be back on on Monday :)
Forum: Bioinformatics 10-20-2011, 12:17 PM
Replies: 2
Views: 1,218
Posted By rudi283
splicing predicton for NGS data

Hi,
I was wondering if you know any free tool for splicing prediction for NGS data? All tools I found required pasting sequence of the gene + sequence with mutation. I need to analyze several...
Forum: Bioinformatics 09-23-2011, 04:36 AM
Replies: 0
Views: 1,106
Posted By rudi283
splice sites-annotation

I need to annotate my human ref seq with splice sites (ideally donor/acceptor sites). I'm not quite sure if it's possible to just download it from somewhere:confused:. Could you please help me?...
Forum: Bioinformatics 05-25-2011, 01:51 AM
Replies: 0
Views: 823
Posted By rudi283
Galaxy-aa changes

Hi,
I was wondering if there is an option in Galaxy to filter out the SNPs which cause amino acid changes and/ or which aa is changed into what.
I filtered pileup but the information I get it's not...
Forum: Bioinformatics 04-15-2011, 02:44 AM
Replies: 3
Views: 1,834
Posted By rudi283
This time is not good as well:( I don't have an...

This time is not good as well:( I don't have an error but the file is empty...
Looks like it's because when I try to generate pileup I get 3 columns with '0' values...

I'm not sure why :( Am I...
Forum: Bioinformatics 04-14-2011, 11:07 PM
Replies: 3
Views: 1,834
Posted By rudi283
Thank you for the reply! I'm trying to do the...

Thank you for the reply!
I'm trying to do the same for my other data as maybe there is something wrong with the data I uploaded to Galaxy. If it will be the same I'm going to do what you suggested....
Forum: Bioinformatics 04-13-2011, 01:44 AM
Replies: 3
Views: 1,834
Posted By rudi283
Galaxy-filter pileup error

Hi,
The aim of my work now is to find SNPs in my dataset from Illumina GAII ( paired end) but when tried to filter pileup got this:

16: Filter pileup on data 14
An error occurred running this...
Forum: Illumina/Solexa 04-11-2011, 05:37 AM
Replies: 19
Views: 6,130
Posted By rudi283
right, but if you could let us know anyway how...

right,
but if you could let us know anyway how did it work would be great
thanks
Forum: Illumina/Solexa 04-11-2011, 05:06 AM
Replies: 19
Views: 6,130
Posted By rudi283
Have you tried an Array-Based Capture as well?

Have you tried an Array-Based Capture as well?
Forum: Illumina/Solexa 04-08-2011, 02:27 AM
Replies: 19
Views: 6,130
Posted By rudi283
Hi, Have you tried to multiplex more than 4...

Hi,
Have you tried to multiplex more than 4 samples?
Forum: Bioinformatics 03-29-2011, 07:22 AM
Replies: 0
Views: 1,183
Posted By rudi283
coverage and SNP detection

Hi,

I was wondering if there is a standard rule about coverage and SNP detection. How many reads (paired end) do I need to be able to say that's a SNP. I heard that need to be above 30 but I'm a...
Forum: Bioinformatics 03-29-2011, 07:04 AM
Replies: 5
Views: 7,400
Posted By rudi283
I've tried to do something similar with gff file...

I've tried to do something similar with gff file and it works fine for me. Just need to make sure that the information in each column in excel spreadsheet is ok. I coppied it into 010 Editor and...
Forum: Bioinformatics 03-06-2011, 03:21 AM
Replies: 3
Views: 2,048
Posted By rudi283
I'm still confused:( So is it normal, such...

I'm still confused:( So is it normal, such differences?
Forum: Bioinformatics 03-05-2011, 11:10 AM
Replies: 3
Views: 2,048
Posted By rudi283
mysterious exons from UCSC

Hi,
I used UCSC to get chr coordinates (hg19)for all exons of genes which Iím interested in.
I annotated the coordinates on refseq (chromosome seq from UCSC, hg19) and saw that the some of them...
Forum: Bioinformatics 03-05-2011, 10:49 AM
Replies: 4
Views: 7,981
Posted By rudi283
Thanks for the answers! I was going to use the...

Thanks for the answers!
I was going to use the UCSC and download a file with SNPs in gtf format but looks like the latest - dbSNP132 has not been added to UCSC yet:(
I'll try with the
1) EnsEMBL...
Forum: Bioinformatics 03-02-2011, 05:46 AM
Replies: 4
Views: 7,981
Posted By rudi283
need help with converting VCF to GTF/GFF format

Hi,
I need to convert my vcf (from ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/v4.0/) file to gff/gtf format to be able to use it for annotating my refseq with SNPs.
Is there any tool I...
Forum: Bioinformatics 03-02-2011, 04:53 AM
Replies: 14
Views: 5,496
Posted By rudi283
I'll try. I was wondering if you may know how...

I'll try.
I was wondering if you may know how could I convert the vcf file to gff/gtf format-I need to have the SNPs in this format to be able to annotate it on the refseq
Forum: Bioinformatics 03-01-2011, 09:25 AM
Replies: 14
Views: 5,496
Posted By rudi283
You're right I was looking on the wrong thing. ...

You're right I was looking on the wrong thing.
So I guess will be ok if I annotate the refseq from NCBI with the SNPs from ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/v4.0/ ?
Thank you...
Forum: Bioinformatics 03-01-2011, 06:13 AM
Replies: 14
Views: 5,496
Posted By rudi283
I downloaded the vcf file and looks like there...

I downloaded the vcf file and looks like there are more SNPs that I've got from UCSC which is great.
I try to compare information for one of the genes, to check how big the differences are between...
Forum: Bioinformatics 03-01-2011, 05:04 AM
Replies: 14
Views: 5,496
Posted By rudi283
I'm looking for the nucleotide changes in my...

I'm looking for the nucleotide changes in my samples - genes which I'm interested in and I would like to compare the results with SNPs which are already in databases.
Coordinates to design probes...
Forum: Bioinformatics 03-01-2011, 04:33 AM
Replies: 14
Views: 5,496
Posted By rudi283
Thank you very much for the answer! So could I...

Thank you very much for the answer!
So could I use refseq from NCBI and annotate it with SNPs (131) from UCSC if the coordinates are the same anyway?
Forum: Bioinformatics 03-01-2011, 03:07 AM
Replies: 14
Views: 5,496
Posted By rudi283
I'm confused even more now:( Does that mean...

I'm confused even more now:(
Does that mean that the chr coordinates are not stable between these two (hg19 and GRCh37)?
As for the annotations I need to see only the genes/exons and probably SNPs...
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