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Forum: Bioinformatics 02-25-2018, 11:19 AM
Replies: 6
Views: 1,892
Posted By jgibbons1
Try assembling raw PacBio reads with Canu, then...

Try assembling raw PacBio reads with Canu, then polish the assembly using the Illumina reads with Pilon.
Forum: Illumina/Solexa 02-24-2018, 12:50 PM
Replies: 2
Views: 1,049
Posted By jgibbons1
I had not thought about it in that way. Thanks!...

I had not thought about it in that way. Thanks! This is very helpful.
Forum: Illumina/Solexa 02-23-2018, 11:11 AM
Replies: 2
Views: 1,049
Posted By jgibbons1
nextera xt for 30 Mb genome

Hi all,

I was wondering if anyone has experience or has tested using the nextera xt kit for moderately sized eukaryotic genomes (20 - 40 Mb).

Any feedback would be greatly appreciated!

JG
Forum: Sample Prep / Library Generation 01-09-2016, 10:59 AM
Replies: 1
Views: 1,420
Posted By jgibbons1
Covaris M220 service plan

Hi all,

Our department is considering purchasing a Covaris M220 so we can begin generating libraries in house. A one year service plan is ~$2000 and we're wondering if purchasing the plan is worth...
Forum: Bioinformatics 08-12-2015, 10:42 AM
Replies: 2
Views: 1,099
Posted By jgibbons1
Thanks for these suggestions. I actually haven't...

Thanks for these suggestions. I actually haven't explored bcftools or freebayes so should have a busy few days :)

I will post an update once I come to a satisfactory solution.
Forum: Bioinformatics 08-11-2015, 02:35 PM
Replies: 2
Views: 1,099
Posted By jgibbons1
mpileup to STRUCTURE

Hi all,
Thought I would see if anyone has a different (better!) pipeline for collecting a set of SNPs from many bam files for use with STRUCTURE or other population genetic software. The end goal is...
Forum: Literature Watch 07-14-2014, 12:00 PM
Replies: 6
Views: 2,041
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, 12:13 PM
Replies: 2
Views: 2,507
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, 02:22 PM
Replies: 4
Views: 1,011
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, 01:27 PM
Replies: 4
Views: 1,011
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, 09:07 AM
Replies: 12
Views: 3,387
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, 08:05 PM
Replies: 12
Views: 3,387
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, 10:28 AM
Replies: 12
Views: 3,387
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, 11:09 AM
Replies: 4
Views: 1,768
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, 11:01 AM
Replies: 1
Views: 964
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, 08:09 AM
Replies: 10
Views: 2,340
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, 08:07 AM
Replies: 10
Views: 2,340
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, 01:45 PM
Replies: 12
Views: 4,104
Posted By jgibbons1
Ahhh...you're right! Whoops...

Ahhh...you're right! Whoops...
Forum: Bioinformatics 11-06-2013, 07:33 AM
Replies: 12
Views: 4,104
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, 03:44 PM
Replies: 5
Views: 1,423
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, 08:42 AM
Replies: 2
Views: 1,415
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, 08:04 AM
Replies: 2
Views: 1,415
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, 06:54 AM
Replies: 2
Views: 1,716
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, 06:52 AM
Replies: 1
Views: 913
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, 10:23 AM
Replies: 4
Views: 5,616
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...
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