SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 127
Search took 0.03 seconds.
Search: Posts Made By: jgibbons1
Forum: Literature Watch 07-14-2014, 11:00 AM
Replies: 6
Views: 408
Posted By jgibbons1
These are a bit dated but should help: ...

These are a bit dated but should help:
http://mbe.oxfordjournals.org/content/26/12/2731.long...
Forum: Genomic Resequencing 05-01-2014, 11:13 AM
Replies: 2
Views: 1,042
Posted By jgibbons1
Hi Thowell, I ended up using jellyfish and...

Hi Thowell,

I ended up using jellyfish and then used a custom perl script to compare kmer counts between samples. It seemed to work fairly well.
Forum: Bioinformatics 03-14-2014, 01:22 PM
Replies: 4
Views: 294
Posted By jgibbons1
Brian, thanks for the heads up about BBMap! The...

Brian, thanks for the heads up about BBMap! The "minratio" flag sounds like a very nice alternative to arbitrary trimming. I think I'll try both methods and see how they compare.

I was asking if...
Forum: Bioinformatics 03-14-2014, 12:27 PM
Replies: 4
Views: 294
Posted By jgibbons1
bowtie map only first 50 nt of reads

Hi all,

My Data:
Illumina whole genome data from ~160 individuals. Reads were initially 100 nt but after quality trimming I have a distribution of read lengths between 50-100 nt.

My Problem:...
Forum: Bioinformatics 02-21-2014, 08:07 AM
Replies: 12
Views: 812
Posted By jgibbons1
Using only single copy regions of the...

Using only single copy regions of the genome/transcriptome would give you a better idea of the true single copy coverage. When you take the average coverage of the genome/transcriptome, you are also...
Forum: Bioinformatics 02-20-2014, 07:05 PM
Replies: 12
Views: 812
Posted By jgibbons1
That's true, but that is why using the "single...

That's true, but that is why using the "single copy ORFs" would circumvent the problem of mapping quality and falsely mapped reads.
Forum: Bioinformatics 02-20-2014, 09:28 AM
Replies: 12
Views: 812
Posted By jgibbons1
I think you're approach will work fine for rough...

I think you're approach will work fine for rough estimates of high CN genes. However, I think you're going to be underestimating copy number, because you are normalizing high CN ORFs by the mean...
Forum: Bioinformatics 12-19-2013, 10:09 AM
Replies: 4
Views: 898
Posted By jgibbons1
Just out of curiosity, how many reads are you...

Just out of curiosity, how many reads are you trying to assemble? Paired end or single end? Have you quality trimmed your data before assembling?
Forum: Bioinformatics 12-19-2013, 10:01 AM
Replies: 1
Views: 432
Posted By jgibbons1
OrthoMCL would probably be a good place to start....

OrthoMCL would probably be a good place to start.

http://orthomcl.org/orthomcl/
Forum: Bioinformatics 12-06-2013, 07:09 AM
Replies: 10
Views: 1,180
Posted By jgibbons1
If you just want to know how many reads are...

If you just want to know how many reads are covered, you can use the same tool, as it does not report '0' depth values. You can simply subtract "covered" bases from total bases.
Forum: Bioinformatics 12-06-2013, 07:07 AM
Replies: 10
Views: 1,180
Posted By jgibbons1
If I understand you correctly, you'd like to know...

If I understand you correctly, you'd like to know the average coverage of your read set. Is that right?

You may consider using the samtools depth function. This calculates depth for every base of...
Forum: Bioinformatics 11-12-2013, 12:45 PM
Replies: 12
Views: 2,697
Posted By jgibbons1
Ahhh...you're right! Whoops...

Ahhh...you're right! Whoops...
Forum: Bioinformatics 11-06-2013, 06:33 AM
Replies: 12
Views: 2,697
Posted By jgibbons1
Oases has been published... ...

Oases has been published...

http://bioinformatics.oxfordjournals.org/content/early/2012/02/24/bioinformatics.bts094.short

I use it quite a bit and find it to be very good.
Forum: Bioinformatics 11-05-2013, 02:44 PM
Replies: 5
Views: 604
Posted By jgibbons1
If you know how many lines are in your file you...

If you know how many lines are in your file you can use the split command

$ wc -l file.fastq
100 file.fastq

$ split -l 50 file.fastq
Forum: Bioinformatics 08-02-2013, 07:42 AM
Replies: 2
Views: 577
Posted By jgibbons1
Hmmm...have not seen snpEff before but it looks...

Hmmm...have not seen snpEff before but it looks promising.

Thanks for the pointer. I will give this a try.

Any other solutions?
Forum: Bioinformatics 08-02-2013, 07:04 AM
Replies: 2
Views: 577
Posted By jgibbons1
VCF coodinates to Genomic Features from GFF

I think this is a relatively simple question but I haven't been able to figure out a solution yet.

Basically, I have a VCF file of variants and a GFF file of the genome with genomic features. I...
Forum: Sample Prep / Library Generation 08-01-2013, 05:54 AM
Replies: 2
Views: 988
Posted By jgibbons1
The integenX system is pretty nice...that is if...

The integenX system is pretty nice...that is if money isn't an object of course :)

http://integenx.com/products/apollo-324/
Forum: Bioinformatics 08-01-2013, 05:52 AM
Replies: 1
Views: 362
Posted By jgibbons1
Indel calling from population data (pool-seq)

Hi all,
I was wondering if anyone has any particular advice regarding indel calling from a paired-end illumina dataset consisting a pool of gDNA from 20 individuals from a population.

I've been...
Forum: RNA Sequencing 07-16-2013, 09:23 AM
Replies: 4
Views: 4,677
Posted By jgibbons1
I'd say it looks pretty normal to me too....

I'd say it looks pretty normal to me too. Obviously it's nice to have all samples in a tighter range, but it is pretty difficult to do so even with multiple modes of quantification. I recently...
Forum: Bioinformatics 07-16-2013, 09:19 AM
Replies: 8
Views: 628
Posted By jgibbons1
Thanks again for your help. Unfortunately, I am...

Thanks again for your help. Unfortunately, I am not much of a programmer. What I think I'll do is recruit a collaborater from my institution to see if they can help come up with a solution.

I will...
Forum: Bioinformatics 07-16-2013, 08:28 AM
Replies: 8
Views: 628
Posted By jgibbons1
I appreciate your insight. This is pretty...

I appreciate your insight.

This is pretty frustrating. Unfortunately, I am really at a standstill until I can figure out how to generate these p-values. I have about a hundred million of tests to...
Forum: Bioinformatics 07-16-2013, 07:57 AM
Replies: 8
Views: 628
Posted By jgibbons1
Thanks dpryan, I just ran into this answer...

Thanks dpryan,
I just ran into this answer myself from the following post:

https://stat.ethz.ch/pipermail/r-help/2012-January/300250.html

Hmmm...is there a way to change this, I wonder?
Forum: Bioinformatics 07-16-2013, 07:34 AM
Replies: 8
Views: 628
Posted By jgibbons1
Hi mastal, Yes, that is correct. The background...

Hi mastal,
Yes, that is correct. The background frequencies are much larger than the observed frequencies.

Thanks for your suggestion. I will try posting to the R/Bioconducor mailing list.
Forum: Bioinformatics 07-16-2013, 06:49 AM
Replies: 8
Views: 628
Posted By jgibbons1
Contingency tests in R, Error with large numbers

I have been struggling to figure out how to fix this error, and I thought why not try the seqanswers community. I am fairly new to R though, so please forgive me if this is a fairly easy solution.
...
Forum: Bioinformatics 07-16-2013, 05:42 AM
Replies: 12
Views: 1,492
Posted By jgibbons1
Thanks xApple. You're right...I ended up taking...

Thanks xApple. You're right...I ended up taking the average of the quality scores.

I will give your script a shot. Thanks!
Showing results 1 to 25 of 127

 


All times are GMT -8. The time now is 04:12 AM.


Powered by vBulletin® Version 3.8.6
Copyright ©2000 - 2014, Jelsoft Enterprises Ltd.