Forum: Bioinformatics
10-25-2013, 03:13 PM
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Replies: 3
Views: 2,582
Error using vcf-stats
I am trying to figure out the variant statistics from a vcf file using the command:
./vcf-stats NA11881roi_variants.vcf
For which I am getting the following output:
The version "4.1" not...
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Forum: Bioinformatics
10-24-2013, 09:42 PM
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Replies: 0
Views: 1,273
Error while calling variants using samtools
Hello all,
I ran the following command to call variants in a given region of interest of a DNA sequnce:
./samtools-0.1.18/samtools mpileup -g -f hg19-bt2.fa NA11881.roi.sorted.bam > variants.bcf
...
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Forum: Bioinformatics
10-24-2013, 05:24 PM
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Replies: 2
Views: 1,846
Getting mapping statistics from a .bed file
Hello,
I have a .bed file that has the aligned sequence reads for some regions of interest. I want to find the number of reads aligned within the target region. Can anybody please help me on how...
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Forum: Bioinformatics
10-24-2013, 10:18 AM
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Replies: 9
Views: 2,337
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Forum: Bioinformatics
10-23-2013, 08:05 PM
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Replies: 9
Views: 2,337
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Forum: Bioinformatics
10-23-2013, 08:01 PM
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Replies: 9
Views: 2,337
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Forum: Bioinformatics
10-23-2013, 07:49 PM
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Replies: 9
Views: 2,337
I am not getting any output for "head...
I am not getting any output for "head NA11881.fastq"
I am not getting any errors or warnings
I have all the index files in the same directory
yes. I have 8 cpus on my computer
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Forum: Bioinformatics
10-23-2013, 06:46 PM
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Replies: 9
Views: 2,337
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Forum: Bioinformatics
10-23-2013, 06:38 PM
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Replies: 9
Views: 2,337
Help with bowtie2 for a beginner (windows)
Hello,
As I am completely new to the field of Next Generation Sequencing and I have absolutely no background in computers, I need your help in figuring out the mistakes that I am doing while...
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