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Search: Posts Made By: Phantom123
Forum: Bioinformatics 07-19-2012, 08:07 AM
Replies: 0
Views: 728
Posted By Phantom123
Gene sequence from transcript sequence

I have variation information for SNPs and small indels together with the position of the variation relative to the transcript. I also have the transcript sequence because i have the NM_ID of the...
Forum: Bioinformatics 03-29-2012, 01:32 PM
Replies: 4
Views: 4,871
Posted By Phantom123
Thank you.

Thank you.
Forum: Bioinformatics 03-29-2012, 01:31 PM
Replies: 4
Views: 4,871
Posted By Phantom123
UCSC hg 19.

UCSC hg 19.
Forum: Bioinformatics 03-28-2012, 03:11 PM
Replies: 4
Views: 4,871
Posted By Phantom123
Samtools filtering question

I used Samtools and bcftools to generate bcf files and then vcf files from the original BAM file containing RNA-seq data. Some of the publications i have read which make use of Samtools talk of...
Forum: Bioinformatics 03-26-2012, 06:47 AM
Replies: 0
Views: 4,011
Posted By Phantom123
Identifying Somatic mutation candidates question

Suppose my data looks something like this for a particular position in a gene in my sample data.

Reference Normal Tumor
1 A A G
2 A G ...
Forum: Bioinformatics 03-25-2012, 07:16 PM
Replies: 5
Views: 3,831
Posted By Phantom123
Much obliged to Heisman.

Much obliged to Heisman.
Forum: Bioinformatics 03-25-2012, 07:05 PM
Replies: 5
Views: 3,831
Posted By Phantom123
Dear All, the first command that i gave in my...

Dear All,
the first command that i gave in my original post as well as the first command given by heisman work fine on my system.

[These are:

perl convert2annovar.pl in.vcf -format vcf4
...
Forum: Bioinformatics 03-21-2012, 06:31 PM
Replies: 16
Views: 3,548
Posted By Phantom123
i had encountered a similar problem. you need to...

i had encountered a similar problem. you need to install Xcode properly.
Forum: Bioinformatics 03-21-2012, 02:55 PM
Replies: 5
Views: 3,831
Posted By Phantom123
Annotating variants using Annovar question

I have vcf files which i generated using samtools. i wish to annotate variant information in these files using annovar. will the following work?

perl convert2annovar.pl in.vcf -format vcf4
...
Forum: Bioinformatics 03-21-2012, 09:12 AM
Replies: 2
Views: 1,024
Posted By Phantom123
Thank you.

Thank you.
Forum: Bioinformatics 03-21-2012, 08:24 AM
Replies: 2
Views: 1,024
Posted By Phantom123
Tophat Bam file question

Do i have to do any sorting on the BAM file that Tophat generates before i convert it to a bcf/vcf file (using Samtools)?

Thanks for your help.
Forum: Bioinformatics 03-19-2012, 11:54 AM
Replies: 2
Views: 2,324
Posted By Phantom123
thank you.

thank you.
Forum: Bioinformatics 03-19-2012, 11:39 AM
Replies: 2
Views: 2,324
Posted By Phantom123
Samtools BAM to bcf question

Dear All,
i am using the following command to convert a BAM file to a bcf file:

samtools mpileup -uf genome.fa raw.accepted_hits.bam|bcftools view -bvcg - > raw.bcf

i think there is a way to...
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