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Forum: Bioinformatics 11-08-2013, 12:59 PM
Replies: 0
Views: 2,816
Posted By d17
VCF file from aligned fasta?

Is it possible to take a file of aligned fasta reads (say 5kb of fasta format sequence or, even better, multifasta format, including one "reference" sequence) and produce a VCF file showing the...
Forum: Bioinformatics 10-20-2011, 12:56 PM
Replies: 6
Views: 2,839
Posted By d17
Anyone interested in RNA editing and RNA/DNA...

Anyone interested in RNA editing and RNA/DNA differences should definitely take a look at this paper:
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0025842
Forum: Bioinformatics 08-11-2011, 10:30 AM
Replies: 1
Views: 3,759
Posted By d17
Take a look at the DESeq or edgeR packages. Both...

Take a look at the DESeq or edgeR packages. Both of these will take raw counts (not RPKM) and perform statistical tests for differential expression between control and condition.
Forum: Genomic Resequencing 07-11-2011, 05:12 PM
Replies: 27
Views: 16,794
Posted By d17
Could you be more specific about what you mean by...

Could you be more specific about what you mean by good results? Did you compare FreeBayes to any other programs?
Forum: Genomic Resequencing 07-11-2011, 09:19 AM
Replies: 27
Views: 16,794
Posted By d17
I did try FreeBayes, and I was able to get it to...

I did try FreeBayes, and I was able to get it to work over a small region for a single sample, but when I expanded to call SNPs over whole chromosomes for several samples at once it no longer worked...
Forum: RNA Sequencing 06-24-2011, 12:47 PM
Replies: 24
Views: 11,127
Posted By d17
Thanks for pointing that out to me, tldgID! I...

Thanks for pointing that out to me, tldgID!
I would still be curious, though, to find out whether there is any particular reason everyone has chosen negative binomial, or whether it is a historical...
Forum: RNA Sequencing 06-24-2011, 12:36 PM
Replies: 24
Views: 11,127
Posted By d17
Dear Simon (or anyone else who wishes to...

Dear Simon (or anyone else who wishes to comment),

I have a (more general) question related to your excellent description above:
I am wondering about the differences between the negative binomial...
Forum: RNA Sequencing 06-14-2011, 11:08 AM
Replies: 2
Views: 2,532
Posted By d17
Check out Aaron Quinlan's bedtools. The...

Check out Aaron Quinlan's bedtools. The coverageBed utility will get you what you are looking for.
Forum: Bioinformatics 05-08-2011, 10:41 AM
Replies: 3
Views: 2,539
Posted By d17
What is probably happening is that the 2600 minus...

What is probably happening is that the 2600 minus 850 SNPs in your sample (call it sample #1) that are only called in the multi-sample SNP calling run are SNPs that didn't have enough evidence to be...
Forum: Bioinformatics 04-19-2011, 11:29 AM
Replies: 3
Views: 5,574
Posted By d17
If you are doing multi-sample calling with each...

If you are doing multi-sample calling with each sample in a separate BAM, it doesn't always make sense to say that one BAM file gave rise to a particular SNP. For example you could have three samples...
Forum: RNA Sequencing 04-18-2011, 04:01 PM
Replies: 24
Views: 11,127
Posted By d17
Several methods model expression levels using the...

Several methods model expression levels using the negative binomial distribution - see e.g. DESeq, edgeR, baySeq ...
Forum: Bioinformatics 04-18-2011, 03:58 PM
Replies: 5
Views: 1,965
Posted By d17
Try taking a look at this paper: ...

Try taking a look at this paper:
http://www.nature.com/nature/journal/v464/n7289/full/nature08872.html

Their data is available on their website and it is pretty easy to access.
Forum: Introductions 04-16-2011, 09:53 PM
Replies: 4
Views: 1,613
Posted By d17
My response above is answering your question. The...

My response above is answering your question. The answer is that how p is calculated will be program-dependent.

If you have Sanger reads that you are analyzing with Phred the second linked ref in...
Forum: Introductions 04-16-2011, 12:01 AM
Replies: 4
Views: 1,613
Posted By d17
For the original Phred scores you can see how p...

For the original Phred scores you can see how p is calculated from the papers describing the method:
http://www.ncbi.nlm.nih.gov/pubmed/9521921
http://www.ncbi.nlm.nih.gov/pubmed/9521922
However...
Forum: RNA Sequencing 04-06-2011, 01:48 PM
Replies: 8
Views: 3,147
Posted By d17
A possible answer to your problems

If these are indeed the exact commands you used I noticed two errors:
1) In the second command you need to say -bhS to output the header to BAM
2) In the fourth command you should be indexing the...
Forum: Genomic Resequencing 03-18-2011, 01:22 PM
Replies: 27
Views: 16,794
Posted By d17
calling SNPs in haploid genomes

Does anyone have any thoughts on calling SNPs from short read data (e.g. Illumina) in haploid genomes? It seems that many SNP calling programs are set up to deal only with diploid genomes (e.g....
Forum: Bioinformatics 03-09-2011, 02:06 PM
Replies: 10
Views: 4,065
Posted By d17
I'm not sure exactly what you mean by "estimate...

I'm not sure exactly what you mean by "estimate base quality scores". You don't need to estimate quality scores for simulated data as you know the true quality scores. That is, you know the true base...
Forum: Bioinformatics 03-09-2011, 08:06 AM
Replies: 10
Views: 4,065
Posted By d17
Take a look at the dwgsim utility in Nils Homer's...

Take a look at the dwgsim utility in Nils Homer's DNA Analysis package at dnaa.sourceforge.net. It does paired-end reads by default but you could just ignore the file of second reads in each pair to...
Forum: Bioinformatics 02-01-2011, 02:25 PM
Replies: 19
Views: 21,449
Posted By d17
According to the SAM format specification...

According to the SAM format specification (http://samtools.sourceforge.net/SAM1.pdf) , read names must be the same for read pairs. Your read pairs do not seem to follow this rule, so it appears they...
Forum: Bioinformatics 01-27-2011, 10:40 AM
Replies: 8
Views: 3,193
Posted By d17
oldFile is the file of coordinates you want to...

oldFile is the file of coordinates you want to convert (typically BED)
unMapped is a file that is created when you run liftOver: it contains those features in oldFile that did not lift over to the...
Forum: SOLiD 02-20-2010, 05:44 PM
Replies: 4
Views: 2,622
Posted By d17
Thanks for the info. I am still a little...

Thanks for the info. I am still a little confused, though: are the intermediate files generated from only the image files? And then the .csfasta + .qual are the result of filtering for reads that...
Forum: SOLiD 02-12-2010, 02:45 PM
Replies: 4
Views: 2,622
Posted By d17
details of *.csfasta creation

Hi,

I am trying to figure out exactly where a *.csfasta file resulting from an ABI SOLiD run comes from. In particular, I am wondering whether the csfasta files are generated from image files...
Forum: Sample Prep / Library Generation 11-20-2009, 09:19 AM
Replies: 9
Views: 7,806
Posted By d17
Thanks ktabbada! It's useful to hear about...

Thanks ktabbada! It's useful to hear about failures as well as successes.

I wonder what they're doing over at Sanger :confused:! The protocol we're referring to [in the paper listed earlier in...
Forum: Sample Prep / Library Generation 11-17-2009, 01:26 PM
Replies: 9
Views: 7,806
Posted By d17
Update?

Hi Kristina,

Any chance you have an update on whether your subnanomolar libraries worked? I'd be interested to hear how this turned out!

I just stumbled on your thread today and am interested...
Forum: Bioinformatics 04-15-2009, 01:48 PM
Replies: 8
Views: 4,526
Posted By d17
Torst, thanks for your input: Yes, you're...

Torst, thanks for your input:


Yes, you're absolutely right ... but I would be happier if we had Q40's that were correct with 99.99% probability! :)


One strange thing we have is that bases...
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