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Search: Posts Made By: ruchi1621
Forum: Bioinformatics 10-25-2013, 03:13 PM
Replies: 3
Views: 2,584
Posted By ruchi1621
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...
Forum: Bioinformatics 10-24-2013, 09:42 PM
Replies: 0
Views: 1,280
Posted By ruchi1621
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
...
Forum: Bioinformatics 10-24-2013, 05:24 PM
Replies: 2
Views: 1,850
Posted By ruchi1621
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...
Forum: Bioinformatics 10-24-2013, 10:18 AM
Replies: 9
Views: 2,339
Posted By ruchi1621
Hi! I transferred the downloaded the file again...

Hi!
I transferred the downloaded the file again and redid the commands and it worked! Thank you so much for your help! :)
Forum: Bioinformatics 10-23-2013, 08:05 PM
Replies: 9
Views: 2,339
Posted By ruchi1621
You are right. The file is empty. Let me transfer...

You are right. The file is empty. Let me transfer it again and re-try aligning it. I will get back to you regarding the success of the same. Thanks for your help!
Forum: Bioinformatics 10-23-2013, 08:01 PM
Replies: 9
Views: 2,339
Posted By ruchi1621
On entering: ls -lh NA11881.fastq i get ...

On entering:
ls -lh NA11881.fastq

i get

-rw-r--r-- 1 bansalr students 0 Oct 16 14:59 NA11881.fastq
Forum: Bioinformatics 10-23-2013, 07:49 PM
Replies: 9
Views: 2,339
Posted By ruchi1621
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
Forum: Bioinformatics 10-23-2013, 06:46 PM
Replies: 9
Views: 2,339
Posted By ruchi1621
Still the same result.

Still the same result.
Forum: Bioinformatics 10-23-2013, 06:38 PM
Replies: 9
Views: 2,339
Posted By ruchi1621
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...
Showing results 1 to 9 of 9

 


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