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Forum: Bioinformatics 05-14-2015, 11:56 AM
Replies: 16
Views: 2,860
Posted By jwag
Hi Len, I was able to run the RTG variant caller...

Hi Len, I was able to run the RTG variant caller using the bam file produced using BBMap (without removing duplicate mapping reads and without trimming ends after mapping) and it seemed to work well....
Forum: Genomic Resequencing 05-14-2015, 09:55 AM
Replies: 3
Views: 2,239
Posted By jwag
Codeml software for looking at positive selection...

Codeml software for looking at positive selection seems to be pretty popular, which is part of the PAML package. There's a few tutorials online that you can look at.
...
Forum: Bioinformatics 05-13-2015, 01:13 PM
Replies: 16
Views: 2,860
Posted By jwag
Ok great, I'll give the RTG caller a go.

Ok great, I'll give the RTG caller a go.
Forum: Bioinformatics 05-13-2015, 10:24 AM
Replies: 16
Views: 2,860
Posted By jwag
Ah that makes sense-- I will keep the duplicates...

Ah that makes sense-- I will keep the duplicates in this case.

If BBDuk could trim mapped reads and also update the CIGAR string at the same time, that would be super useful. I've yet to find...
Forum: Bioinformatics 05-13-2015, 10:02 AM
Replies: 16
Views: 2,860
Posted By jwag
Thanks for the reply Brian. The DNA was prepared...

Thanks for the reply Brian. The DNA was prepared using a Nexetra kit which I believe involves a few cycles of PCR. So just to double check, I shouldn't remove duplicates since I'm trying to...
Forum: Bioinformatics 05-13-2015, 09:18 AM
Replies: 16
Views: 2,860
Posted By jwag
Hi again, I wanted to update progress for anyone...

Hi again, I wanted to update progress for anyone still following the thread. I've been playing with BBmap, which appears to be doing very well with gapped alignments. I looked into the caller by...
Forum: Genomic Resequencing 05-13-2015, 09:01 AM
Replies: 3
Views: 2,239
Posted By jwag
You might be able to look at amino-acid (codon)...

You might be able to look at amino-acid (codon) specific positive selection, although this might work better if you find the gene in multiple other species for comparison. You might also be able to...
Forum: Bioinformatics 05-13-2015, 08:51 AM
Replies: 2
Views: 693
Posted By jwag
You could export it and filter out those tagged...

You could export it and filter out those tagged as being the reference allele. I've exported it as an excel sheet and filtered it that way before, when I've used CLC.
Forum: Bioinformatics 05-06-2015, 10:08 AM
Replies: 16
Views: 2,860
Posted By jwag
Hi Matt, I will give that a try . I'm...

Hi Matt,

I will give that a try . I'm currently using Geneious for SNP calling -- it seems to be working pretty well. Do you know if people typically remove duplicate reads in an alignment prior...
Forum: Bioinformatics 05-04-2015, 09:57 AM
Replies: 16
Views: 2,860
Posted By jwag
Hi all, Here's an update. I used the...

Hi all,

Here's an update. I used the pipeline suggested by Brian to allow for large gaps in bbmap (k=10 maxindel=400 tipsearch=300 slow). I then tried various callers to see what they would do...
Forum: Bioinformatics 04-29-2015, 09:59 AM
Replies: 16
Views: 2,860
Posted By jwag
Hi Brian, Thanks for the reply. I used...

Hi Brian,

Thanks for the reply. I used BBMap according to your suggestions. The BBmerge merged ~95% of my reads, then I mapped it to my reference using k=10 (props for making the program very...
Forum: Bioinformatics 04-28-2015, 09:12 AM
Replies: 16
Views: 2,860
Posted By jwag
Quantifying mitochondrial deletions in a single individual -- is it possible?

Hi all, I've sequenced the mitochondria of an individual using Illumina (100bp PE, insertion size is 150-180nt). So far, I've been able to determine that its mitochondria has a heteroplasmy...
Forum: Bioinformatics 11-05-2014, 07:54 AM
Replies: 0
Views: 608
Posted By jwag
Compiling static binary of Allpaths-LG

Hello,

My computing resource department doesn't seem to want to update the GCC compiler on our server to version >4.7, so I can't compile the latest Allpaths-LG genome assembler and use it. They...
Forum: General 08-01-2014, 09:17 AM
Replies: 10
Views: 2,499
Posted By jwag
You could check out Practical Computing for...

You could check out Practical Computing for Biologists (http://www.sinauer.com/catalog/biology/scientific-computing/practical-computing-for-biologists.html). Gives a pretty good intro into using...
Forum: General 08-01-2014, 09:01 AM
Replies: 2
Views: 4,531
Posted By jwag
Thanks, that really helps. I've recently de novo...

Thanks, that really helps. I've recently de novo assembled a fish genome, so I'm trying to compare how close others have come to assembling a complete genome (with respect to the theoretical genome...
Forum: General 07-31-2014, 08:30 AM
Replies: 2
Views: 4,531
Posted By jwag
Whole assembly vs Golden path length in Ensembl?

This has been puzzling me for a while and I haven't been able to find a good answer for this. On the Ensembl website (ensembl.org/) you can find reference genomes for various species. What confuses...
Forum: Sample Prep / Library Generation 02-21-2014, 10:02 AM
Replies: 8
Views: 1,760
Posted By jwag
I might just wait until PacBio or SMRTcells...

I might just wait until PacBio or SMRTcells become more affordable... as of right now it's about $6k to do 1X coverage of PacBio for a 1.6 GB genome.
Forum: Bioinformatics 02-21-2014, 09:50 AM
Replies: 15
Views: 5,007
Posted By jwag
I have used Allpaths-LG to assemble a ~1.6 GB...

I have used Allpaths-LG to assemble a ~1.6 GB vertebrate genome. It used up all of our 760 GB RAM and took about a week.

I don't think you'd want to run Allpaths-LG on a cluster because it is only...
Forum: Sample Prep / Library Generation 02-21-2014, 09:47 AM
Replies: 8
Views: 1,760
Posted By jwag
The genome of interest is highly repetitive...

The genome of interest is highly repetitive (estimated 21% tandem repeats, 42% repetitive). Unfortunately, there isn't a related genome available. I wanted to be able to do structural rearrangement...
Forum: Sample Prep / Library Generation 02-21-2014, 09:14 AM
Replies: 8
Views: 1,760
Posted By jwag
I'm using Illumina technology for sequencing. I...

I'm using Illumina technology for sequencing. I looked into PacBio, but the genome I'm trying to sequence is 1.6 GB, far too expensive for PacBio currently even only at 1X coverage. I might just...
Forum: Sample Prep / Library Generation 02-18-2014, 06:12 PM
Replies: 8
Views: 1,760
Posted By jwag
Anyone had luck with Fosmid library prep kits?

Hi -- I was wondering if anyone has had any luck with making 40kb jumping libraries using a Fosmid kit. I was looking at this NxSeq 40kb mate pair cloning kit ...
Forum: Pacific Biosciences 02-04-2014, 04:48 PM
Replies: 7
Views: 3,579
Posted By jwag
Hi Wallysb01, thanks for your reply. We are...

Hi Wallysb01, thanks for your reply. We are planning on using Allpaths LG to assemble our genome, which has specific library requirements. From what I can tell, there doesn't seem to be an...
Forum: Pacific Biosciences 02-04-2014, 12:02 PM
Replies: 7
Views: 3,579
Posted By jwag
Would PacBio RII reads be useful at 1X?

Hi All, I'm planning on sequencing a highly repetitive vertebrate genome (~1.6 GB genome, ~42% repetitive) using mostly Illumina reads (50X short insert and 50X 3kb insert, PE 150bpx2 reads). I was...
Forum: Bioinformatics 08-16-2013, 03:41 PM
Replies: 12
Views: 2,382
Posted By jwag
I just checked the prinseq website and it looks...

I just checked the prinseq website and it looks like it does indeed support paired output now. I might start using it again, because I like how it lets you choose the number of N's to leave in a...
Forum: Bioinformatics 08-15-2013, 11:16 AM
Replies: 12
Views: 2,382
Posted By jwag
I've used Prinseq for trimming, but it doesn't...

I've used Prinseq for trimming, but it doesn't maintain paired read order, so I stopped using it.

I have not used Prinseq for statistics (I've only used FastQC) so I couldn't comment on any...
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