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Search: Posts Made By: BAMseek
Forum: Bioinformatics 09-19-2013, 10:13 PM
Replies: 6
Views: 3,962
Posted By BAMseek
Hey Eric, My guess would be that if a read...

Hey Eric,

My guess would be that if a read is split (such as spanning a splice junction), then that read may count towards the coverage for the entire interval, even the skipped bases. This link...
Forum: Service Providers 07-24-2013, 09:46 PM
Replies: 15
Views: 4,992
Posted By BAMseek
Sure, he might have had different intentions, but...

Sure, he might have had different intentions, but unless you are the same person as him, then we can only conjecture. For me, it was misleading.
Forum: Service Providers 07-24-2013, 09:22 PM
Replies: 15
Views: 4,992
Posted By BAMseek
I appreciate tsa for pointing that out. I don't...

I appreciate tsa for pointing that out. I don't see anything wrong with making it explicit. Otherwise, it would have looked like an endorsement from a third-party.

Justin
Forum: Bioinformatics 07-23-2013, 08:02 PM
Replies: 11
Views: 4,916
Posted By BAMseek
You are correct, there isn't a search/find...

You are correct, there isn't a search/find function available. To do that, there is a lot of power and flexibility from using samtools and grep in the command line. You might try something like...
Forum: Bioinformatics 07-10-2013, 06:37 PM
Replies: 7
Views: 4,414
Posted By BAMseek
I would suggest setting the -d flag very high...

I would suggest setting the -d flag very high (like 100 million) in order to get accurate coverage results. If your coverage at a position is above the threshold, then the reported depth may not be...
Forum: Bioinformatics 06-28-2013, 12:43 PM
Replies: 4
Views: 12,388
Posted By BAMseek
Aligning reads to a genome can be viewed in the...

Aligning reads to a genome can be viewed in the general context of approximate string matching. The goal is to find a pattern (the short-read) in a large text or corpus (the genome), allowing for...
Forum: Bioinformatics 06-19-2013, 12:16 PM
Replies: 1
Views: 3,360
Posted By BAMseek
I found the latex for it: ...

I found the latex for it:

https://github.com/samtools/sam-spec/blob/master/SAMv1.tex

Looks like you'll have to convert latex to pdf if you want to make it more readable.

Justin
Forum: General 06-13-2013, 09:42 AM
Replies: 4
Views: 1,327
Posted By BAMseek
It seems to me that for all practical purposes,...

It seems to me that for all practical purposes, the Myriad gene patents are upheld (wall street seems to agree with that too). Even though isolated DNA is not eligible for patents like it was...
Forum: Bioinformatics 05-23-2013, 03:17 PM
Replies: 2
Views: 826
Posted By BAMseek
Samtools has a maximum depth cut-off in order to...

Samtools has a maximum depth cut-off in order to limit the amount of memory required, which leads to some odd behavior when you hit that max. I think the max is 8,000 and it looks like you are close...
Forum: Clinical Sequencing 05-23-2013, 12:34 PM
Replies: 0
Views: 5,395
Posted By BAMseek
Website to find variants associated with a disease

Hi all,

I'll be moving out to the Bay area soon to work for Amazon, so quite a shift in my career path. There is a project I was working on that I didn't get as far as I would like but thought I...
Forum: Bioinformatics 05-21-2013, 12:48 PM
Replies: 11
Views: 4,916
Posted By BAMseek
BAMseek is a text viewer that lets you see the...

BAMseek is a text viewer that lets you see the actual text within a BAM file (such as what you would get with samtools view). So probably not what you are looking for if you are looking for a new...
Forum: Bioinformatics 05-18-2013, 11:07 PM
Replies: 2
Views: 2,241
Posted By BAMseek
The B flag is an addition to the BAM/SAM...

The B flag is an addition to the BAM/SAM specifications to support arrays of various types. Support for the B flag was added to Picard-Tools 1.51...
Forum: Bioinformatics 04-09-2013, 06:26 AM
Replies: 2
Views: 1,334
Posted By BAMseek
Take a look at Mutalyzer...

Take a look at Mutalyzer (https://mutalyzer.nl/positionConverter) . I copied and pasted "NM_001100.3:c.7G>T" into the box and get NC_000001.10:g.229568856C>A as the result.

Justin
Forum: Bioinformatics 03-29-2013, 03:50 PM
Replies: 7
Views: 2,656
Posted By BAMseek
Hmm, it's odd that samtools view gives you...

Hmm, it's odd that samtools view gives you nothing but samtools view -h gives you lots of lines. So can you take one of those positions, and go to it in IGV? Also, what are the results of samtools...
Forum: Bioinformatics 03-29-2013, 12:00 PM
Replies: 7
Views: 2,656
Posted By BAMseek
That's not good. What is the size of your BAM...

That's not good. What is the size of your BAM file? Also, try "samtools view -h <input.bam>" (the -h flag will also print out header information). Getting nothing might because the file is blank...
Forum: Bioinformatics 03-28-2013, 01:51 PM
Replies: 7
Views: 2,656
Posted By BAMseek
Try looking at the first few lines of the bam...

Try looking at the first few lines of the bam file



The 3rd and 4th columns are the chromosome and position. Pick one of those locations and go to it in IGV to see if you can find that read. ...
Forum: Bioinformatics 03-22-2013, 01:03 PM
Replies: 2
Views: 947
Posted By BAMseek
You might want to check out dwgsim...

You might want to check out dwgsim (http://sourceforge.net/apps/mediawiki/dnaa/index.php?title=Whole_Genome_Simulation) by Nils Homer. It allows you to specify a reference and a list of mutations...
Forum: Bioinformatics 03-21-2013, 08:56 PM
Replies: 3
Views: 1,011
Posted By BAMseek
A back-of-the-envelope approach might be to model...

A back-of-the-envelope approach might be to model it like rolling a 4-sided die, where the probabilities of A,C,G,T are independent and based on the global GC content of that species. If you want to...
Forum: Bioinformatics 03-13-2013, 06:05 PM
Replies: 8
Views: 7,905
Posted By BAMseek
This is a guess, but it may be that SNPs were...

This is a guess, but it may be that SNPs were called on the samples individually, and then those VCFs were merged into one multi-sample VCF. Provided there was sufficient evidence at a position for...
Forum: Bioinformatics 03-13-2013, 05:36 PM
Replies: 8
Views: 7,905
Posted By BAMseek
AFAIK, "./." means the call at that position is...

AFAIK, "./." means the call at that position is missing. It could be missing for a variety of reasons. It might be missing because a call was made, but it didn't meet some threshold and was filtered...
Forum: Bioinformatics 02-11-2013, 07:05 PM
Replies: 9
Views: 7,100
Posted By BAMseek
Maybe try the suggestions from this stackoverflow...

Maybe try the suggestions from this stackoverflow post:

http://stackoverflow.com/questions/2685887/where-is-gcc-on-osx-i-have-installed-xcode-already

I would especially try the one where it...
Forum: Bioinformatics 02-11-2013, 03:16 PM
Replies: 9
Views: 7,100
Posted By BAMseek
The errors you are getting (no stdio.h, stdlib.h,...

The errors you are getting (no stdio.h, stdlib.h, . . .) would make me believe that you don't have gcc installed. What do you get if you type "which gcc" in the terminal? It should give you the...
Forum: RNA Sequencing 01-28-2013, 07:31 AM
Replies: 16
Views: 3,293
Posted By BAMseek
I think that the coloring means that the paired...

I think that the coloring means that the paired read was aligned to a different chromosome. If you hadn't already put in the -A flag for anomalous reads, I would have guessed that to be the cause of...
Forum: RNA Sequencing 01-27-2013, 05:29 PM
Replies: 16
Views: 3,293
Posted By BAMseek
Looks like from your mpileup output that the...

Looks like from your mpileup output that the calls are

chr1 205131282 T
chr1 205131283 T

This lines up with IGV, so looks like that is fine. The only other thing I can think to check would be...
Forum: Bioinformatics 01-26-2013, 10:47 AM
Replies: 2
Views: 2,045
Posted By BAMseek
I have run into something like this, too. An...

I have run into something like this, too. An insertion occurs between two adjacent positions. I think VCF lists the position before the insertion. So for example, if there was a substitution followed...
Showing results 1 to 25 of 124

 


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