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Forum: Bioinformatics 11-17-2015, 02:11 AM
Replies: 9
Views: 3,283
Posted By student-t
So, how much % of the total variance should be...

So, how much % of the total variance should be expected?
Forum: Metagenomics 06-04-2015, 10:39 PM
Replies: 5
Views: 2,067
Posted By student-t
Brian, do know any paper that reviews it? I'm...

Brian, do know any paper that reviews it? I'm interested in knowing more.
Forum: Metagenomics 06-04-2015, 04:48 PM
Replies: 5
Views: 2,067
Posted By student-t
This is also known as virtual memory, where the...

This is also known as virtual memory, where the hard-disk space is being used for paging.
Forum: Metagenomics 06-01-2015, 07:26 PM
Replies: 5
Views: 2,067
Posted By student-t
The approximate memory requirement is: number of...

The approximate memory requirement is: number of nodes * 416 bytes because 416 bytes is the memory required for a node data-structure in C.
Forum: Bioinformatics 05-19-2015, 04:52 PM
Replies: 1
Views: 1,125
Posted By student-t
The answer is it depends. Note that they use a...

The answer is it depends. Note that they use a very different statistical model, so it's not fair to compare the p-values. You'll have to understand the statistical model before you can conclude...
Forum: Bioinformatics 05-19-2015, 04:47 PM
Replies: 3
Views: 713
Posted By student-t
Can you just visualize them on a viewer such as...

Can you just visualize them on a viewer such as IGV?
Forum: Bioinformatics 05-18-2015, 04:28 AM
Replies: 4
Views: 1,113
Posted By student-t
I'm doing it myself right now. I'm post a sample...

I'm doing it myself right now. I'm post a sample script that starts from the very beginning soon.
Forum: Bioinformatics 05-17-2015, 11:02 PM
Replies: 4
Views: 1,113
Posted By student-t
There is a nice example in the vignette. What...

There is a nice example in the vignette. What don't you give it a go? Put your commands here if you got stuck. Basically, you'll need to read in your count matrix file and specify the meta-data for...
Forum: Bioinformatics 05-12-2015, 06:06 PM
Replies: 14
Views: 3,127
Posted By student-t
What k-mer size have you specified to velvet?

What k-mer size have you specified to velvet?
Forum: De novo discovery 05-12-2015, 05:59 PM
Replies: 7
Views: 4,242
Posted By student-t
There're a few solutions to calculating metrics...

There're a few solutions to calculating metrics for an assembly.

1. https://github.com/ajmazurie/velvet-stats
2. Biopieces...
Forum: Bioinformatics 05-10-2015, 11:13 PM
Replies: 19
Views: 124,456
Posted By student-t
N50 is a good but not perfect statistic to...

N50 is a good but not perfect statistic to measure how well a de-novo assembly it is. We prefer a set of large contigs because they give us better confidence. This statistics tells us that.
Forum: Bioinformatics 04-08-2015, 03:30 AM
Replies: 4
Views: 1,867
Posted By student-t
For reference (using the htslib library) ...

For reference (using the htslib library)



#include <htslib/sam.h>

auto f = sam_open(file.c_str(), "r");
auto h = sam_hdr_read(f);
auto t = bam_init1();
Forum: Bioinformatics 04-08-2015, 03:25 AM
Replies: 0
Views: 950
Posted By student-t
Bug? Do we need a header for a SAM?

I'm using the htslib C library for parsing my SAM files (also used by the samtools project). The library fails if there is no header in a SAM file. However, header is optional as specified in the...
Forum: Bioinformatics 04-03-2015, 04:38 PM
Replies: 7
Views: 8,647
Posted By student-t
Yeah, using an absolute path works.

Yeah, using an absolute path works.
Forum: Bioinformatics 03-27-2015, 11:44 PM
Replies: 3
Views: 1,045
Posted By student-t
I have read the documentation but still having...

I have read the documentation but still having problems. What I'm doing now is that, I'm simulating variants, mutations etc from a reference genome. I'd expect I'd see something from the GATK tool. I...
Forum: Bioinformatics 03-26-2015, 03:21 PM
Replies: 3
Views: 1,045
Posted By student-t
Protocol for finding variants in GATK

Hi,

I'm looking for a way to use GATK for finding variants. Unfortunately, their documentation is poor and misleading. The commands that they present on their presentation slides are out-of-dated....
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