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Forum: Bioinformatics 02-08-2011, 05:02 AM
Replies: 7
Views: 5,635
Posted By andrehorta
Help!

anyone?????
Forum: Bioinformatics 02-07-2011, 05:11 AM
Replies: 7
Views: 5,635
Posted By andrehorta
I used the command: bowtie -p 4 /rs4244385A ...

I used the command: bowtie -p 4 /rs4244385A

And reads that failed to align: (100.00%)

Can help me?
Forum: Bioinformatics 02-07-2011, 04:52 AM
Replies: 0
Views: 2,745
Posted By andrehorta
Smile BOWTIE - Build Indexes - tutorial

Hi Everyone,

I would like to build a BOWTIE index for the SNP rs4244285A. I created a text file with this characteres:
>rs4244285-aleloA...
Forum: Bioinformatics 02-04-2011, 10:03 AM
Replies: 17
Views: 29,845
Posted By andrehorta
Dears, i need your help! When i typed the...

Dears, i need your help!

When i typed the command: bowtie -p 4 rs4244385A

The folow message is returned:

could not locate bowtie index corresponding to basename rs4244385A

I was try to...
Forum: Bioinformatics 01-13-2011, 10:02 AM
Replies: 27
Views: 6,984
Posted By andrehorta
OK, now i used SAMTOOLS to sort snp in...

OK, now i used SAMTOOLS to sort snp in HG00096.BAM and it's generated HG00096_snp.sorted.BAM. I need the HG000096.fna, e.g:

samtools pileup -cv -f genomes/NC_008253.fna ec_snp.sorted.bam
Forum: Bioinformatics 01-13-2011, 08:07 AM
Replies: 27
Views: 6,984
Posted By andrehorta
How can i use this data with BOWTIE and...

How can i use this data with BOWTIE and BRCA-DIAGNOSTIC? What they will produce?
Forum: Bioinformatics 01-13-2011, 08:02 AM
Replies: 27
Views: 6,984
Posted By andrehorta
Hi Laura! Thank you very much with your...

Hi Laura!

Thank you very much with your attention! I need:

1) Download one genome from 1000 genomes project
2) I need use BRCA-DIAGNOSTIC or/and BOWTIE (i know how i use them, i follow the...
Forum: Bioinformatics 01-13-2011, 07:38 AM
Replies: 27
Views: 6,984
Posted By andrehorta
Hi. I'm newer whith genome. I need yours...

Hi.

I'm newer whith genome. I need yours help. I was downloaded a sequence_read from 1000 genome project (ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/data/HG00096/), and i sow two foldres,...
Forum: Bioinformatics 01-13-2011, 04:19 AM
Replies: 0
Views: 1,662
Posted By andrehorta
Exclamation Bowtie vs 1000 genome project

Dears,

How can i work with Bowtie and genome from "1000 genome project"? I dowloaded this genome: ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/data/HG00096/sequence_read/

Now, what i can do?...
Forum: Bioinformatics 01-13-2011, 03:01 AM
Replies: 0
Views: 1,631
Posted By andrehorta
Unhappy What do i do with the generated files? BRCA-DIAGNOSTIC

Good Morning.

My name's André Horta, i'm from Brazil, i'm doing pós-doc in Molecular Medicine at UFMG. I follow the instructions (http://cbcb.umd.edu/software/BRCA-diagnostic/), and everything...
Forum: Bioinformatics 01-12-2011, 04:37 AM
Replies: 0
Views: 1,275
Posted By andrehorta
Lightbulb brca_diagnostic in Windows

It's possible?

Because Windows don't has the command CAT.

Anybody use brca_diagnostic?
Forum: Bioinformatics 01-12-2011, 04:34 AM
Replies: 2
Views: 1,761
Posted By andrehorta
I don't know too. Process...

I don't know too.

Process C:/ufmg/brca_diagnostic/FASTQ/SRR062634.filt.fastq
# reads processed: 308846
# reads with at least one reported alignment: 833 (0.27%)
# reads that failed to align:...
Forum: Introductions 01-12-2011, 04:31 AM
Replies: 0
Hi
Views: 858
Posted By andrehorta
Smile Hi

Hi!

My name is André Horta, I'm from Brazil - Belo Horizonte, i'm student of medicine doctorate (pós-graduate).

I'm using Bowtie and Crossbow.

By
Forum: Bioinformatics 01-12-2011, 04:28 AM
Replies: 6
Views: 8,702
Posted By andrehorta
Hi! Are you using Linux or Windows. I can...

Hi!

Are you using Linux or Windows. I can help you!

André
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