SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 14 of 14
Search took 0.01 seconds.
Search: Posts Made By: vaibhavvsk
Forum: Bioinformatics 04-14-2016, 03:48 AM
Replies: 0
Views: 1,183
Posted By vaibhavvsk
Question How to generate RO ad AO counts in vcf file to calculate altered allele frequency.

I'm want to calculate Alternate Allele Frequency from the vcf file. I came to know that it can be calculated based on RO(Reference allele observation count) and AO(Alternate allele observation count)...
Forum: Bioinformatics 02-10-2016, 07:27 PM
Replies: 0
Views: 1,346
Posted By vaibhavvsk
Question mpileup core dumped error with input fasta aligned bamfile.

I did bwa mem human alignment with single end fasta file. I tried running samtools mpileup & i'm getting same error as mentioned in thread as :Aborted (core dumped)
Command used was :
samtools...
Forum: Bioinformatics 12-30-2015, 02:38 AM
Replies: 4
Views: 1,301
Posted By vaibhavvsk
As per your quote above my vcf file header shows:...

As per your quote above my vcf file header shows:

My vcf file has been generated through UnifiedGenotyper.

##INFO=<ID=DP,Number=1,Type=Integer,Description="Filtered Depth">
Forum: Bioinformatics 12-28-2015, 08:41 PM
Replies: 4
Views: 1,301
Posted By vaibhavvsk
Question Discrepancy in DP value in vcf file and reads visualization in IGV

A sample variant from my vcf file :

I 27000 . A G 37.88 . AC=2;AF=1.00;AN=2;DP=51;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.0000;MQ=6.53;MQ0=49;QD=0.74 GT:AD:DP:GQ:PL ...
Forum: Illumina/Solexa 12-24-2015, 03:23 AM
Replies: 3
Views: 4,001
Posted By vaibhavvsk
Thumbs up Hey GenoMax it worked for me. Thanks Jessica_L...

Hey GenoMax it worked for me. Thanks Jessica_L too!
Forum: Illumina/Solexa 12-23-2015, 02:23 AM
Replies: 3
Views: 4,001
Posted By vaibhavvsk
Question How to know whether its Read1(Forward) or Read2(Reverse) from fastq contents.

As per fastq file description on wikipedia(https://en.wikipedia.org/wiki/FASTQ_format) Illumina Sequence Identifier format as :
Case A. Standard Illumina Format
Read Identifier :...
Forum: Bioinformatics 07-30-2015, 05:57 AM
Replies: 0
Views: 497
Posted By vaibhavvsk
Problem with job execution when more than 4 jobs are submitted to condor

We are building an application for analyzing NGS data. The application uses the Kepler workflow engine (v 2.4) for workflow execution. We have integrated HT Condor (v.8.2.3) with kepler for grid...
Forum: RNA Sequencing 12-15-2012, 03:43 AM
Replies: 1
Views: 1,358
Posted By vaibhavvsk
Post Tophat Linux x86_64 binary Error

I have downloaded the Linux x86_64 binary (http://tophat.cbcb.umd.edu/downloads/tophat-2.0.6.Linux_x86_64.tar.gz). I'm trying to run tophat on the the data using command given as follows :
...
Forum: General 04-07-2012, 06:17 AM
Replies: 23
Views: 124,094
Posted By vaibhavvsk
That's Great

That's Great
Forum: Bioinformatics 02-20-2012, 08:46 PM
Replies: 11
Views: 34,425
Posted By vaibhavvsk
Hello Alex, I have also same kind of...

Hello Alex,

I have also same kind of experience as with Bgansw

samtools view -F4 sample.bam > sample.mapped.sam

samtools view -f4 sample.bam > sample.unmapped.sam

unmapped file is empty.
Forum: Bioinformatics 01-10-2012, 10:05 PM
Replies: 11
Views: 34,425
Posted By vaibhavvsk
Thanks marcowanger & ulz_peter for your...

Thanks marcowanger & ulz_peter for your guidelines .It can be easily done by shell,Perl or Java.:)
Forum: Bioinformatics 01-10-2012, 08:41 PM
Replies: 11
Views: 34,425
Posted By vaibhavvsk
How to extract mapped and unmapped raw reads from bwa's sam file ?

I have aligned paired end with reference sequence using BWA and got sam output file.I tried picard tools samToFastq tool to convert sam into paired end fastq files but it's for just mapped reads.
I...
Forum: Illumina/Solexa 11-17-2011, 02:54 AM
Replies: 74
Views: 362,881
Posted By vaibhavvsk
Nice Info.

Nice Info.
Forum: Introductions 11-16-2011, 09:22 PM
Replies: 2
Views: 1,810
Posted By vaibhavvsk
Relationship between kmer size and read length and total no.of reads. ?

To start the assembly process we have to set ther kmer size.I'm not clear about the relationship between kmer size,read length and total no.of reads so that i can decide proper kmer size.
Showing results 1 to 14 of 14

 


All times are GMT -8. The time now is 08:20 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO