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Forum: Bioinformatics 09-08-2014, 02:28 AM
Replies: 53
Views: 64,560
Posted By rathankar
calculating coverage depth

Hi

I went thru this post and understood how do we express coverage depth. But I need a small clarification. Does this coverage depth involve mutations in the reads [i mean non matching positions...
Forum: Genomic Resequencing 01-21-2013, 11:36 PM
Replies: 1
Views: 1,036
Posted By rathankar
basic doubts in mapping

I have a doubt in mapping studies
I had taken a set of proteins and obtained the mRNA from NCBI and then converted them in to reads using a perl program. If i want to map them back to the reference...
Forum: Bioinformatics 01-15-2013, 02:20 AM
Replies: 1
Views: 711
Posted By rathankar
CIGAR text not found while mapping

Hi all
I couldnt find the CIGAR tags after mapping ESTs to a reference sequence. Because of this, I am not able to visualize the mapping results in a tablet viewwer. what could be the reason
Forum: General 11-15-2012, 08:35 PM
Replies: 1
Views: 822
Posted By rathankar
contigs or reads for sequence search in a metagenomics run

Dear all
I have a doubt:
In a metagenomics experiment, we have reads sequenced from an environmental sample.

Analysis:
1. assemble these reads and get contigs
2. search these contigs against...
Forum: The Pipeline 08-12-2012, 11:10 PM
Replies: 0
Views: 2,102
Posted By rathankar
ERROR per nucleotide in a set of reads--calculation

How do we calculate the average error per nucleotide in a set of reads. i am currently using pipeline pilot for working on NGS
Forum: Bioinformatics 08-08-2012, 04:27 AM
Replies: 0
Views: 870
Posted By rathankar
doubt in mapping

i did a mapping study using BOWTIE and TOPHAT for a sample read file:
1. The mapped statistics says:
number of genes in the mapping using bowtie: 47
number of repeat regions in the mapping using...
Forum: General 07-26-2012, 10:39 PM
Replies: 5
Views: 1,295
Posted By rathankar
I am an application scientist working for apsara...

I am an application scientist working for apsara innovations currently working on pipeline pilot NGS collection
i have an yeast repository in which the complete genome is downloaded along with its...
Forum: General 07-26-2012, 04:54 AM
Replies: 5
Views: 1,295
Posted By rathankar
is it that before we proceed for analysis, we...

is it that before we proceed for analysis, we need to remove all such regions
Forum: General 07-26-2012, 03:44 AM
Replies: 5
Views: 1,295
Posted By rathankar
introns as a subset of mRNAs

Hi all
can we have introns as a subset of mRNAs. pls let me know.
in yeast genome, if found that a few mRNAs has intronic regions too. how can this be
Forum: Introductions 04-02-2012, 03:35 AM
Replies: 373
Views: 110,245
Posted By rathankar
dear friends I am new member for NGS analysis...

dear friends
I am new member for NGS analysis and have the following data. any help would be appreciated from the members or the administrator of the group
1. i am working on mus musculus and in...
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