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Search: Posts Made By: dacotahm
Forum: Bioinformatics 10-12-2017, 01:00 PM
Replies: 7
Views: 1,521
Posted By dacotahm
It's been a while but I circled back to cleaning...

It's been a while but I circled back to cleaning this transcriptome up.

I don't know the amount of genetic variation, that's something we're planning to dig in to sometime next year.

Anway, I...
Forum: Sample Prep / Library Generation 05-01-2017, 08:33 AM
Replies: 0
Views: 374
Posted By dacotahm
How much gDNA per Drosophila?

Hi, trying to get an idea of maximum yield of gDNA that could be expected from a few insect species.

Does anyone have an estimate for high molecular weight gDNA per # of individuals or per...
Forum: Bioinformatics 02-21-2017, 07:41 AM
Replies: 7
Views: 1,521
Posted By dacotahm
Here's my results if you're interested. ...

Here's my results if you're interested. Dedupe.sh didn't remove as many as I expected from one set, so I'm not sure how to interpret that.

I ran all of the norm and error correction steps on the...
Forum: Bioinformatics 02-19-2017, 12:14 PM
Replies: 4
Views: 1,272
Posted By dacotahm
My plan was to use the long reads with high error...

My plan was to use the long reads with high error rate to bridge scaffolds and then map Illumina on to them, swap bases to favor Illumina, and hopefully fill in some of the Ns
Forum: Bioinformatics 02-16-2017, 12:07 PM
Replies: 4
Views: 1,272
Posted By dacotahm
How to assemble long reads to scaffolds?

I would like to use some long reads from new nanopore data to lengthen and bridge scaffolds in an existing genome release. Does anyone have a recommendation for an assembler that would work well or...
Forum: Bioinformatics 02-07-2017, 11:51 AM
Replies: 7
Views: 1,521
Posted By dacotahm
I'm getting a weird error in bbduk.sh where it...

I'm getting a weird error in bbduk.sh where it says I have unpaired reads.

BBDuk version 36.92
maskMiddle was disabled because useShortKmers=true
Initial:
Memory: max=205801m, free=201506m,...
Forum: Bioinformatics 02-07-2017, 09:54 AM
Replies: 7
Views: 1,521
Posted By dacotahm
Thanks, I'll give that a shot and report my...

Thanks, I'll give that a shot and report my results when finished
Forum: General 02-07-2017, 07:23 AM
Replies: 0
Views: 556
Posted By dacotahm
Cheap size fractionation for nanopore sequencing?

Hello,

I'm doing some 2D nanopore sequencing and I'm a bit disappointed with the number and cost of third-party products recommended in the protocols (specifically 2D Genomic DNA selecting for...
Forum: Bioinformatics 02-02-2017, 11:45 AM
Replies: 7
Views: 1,521
Posted By dacotahm
Cleaning up, merging de novo transcriptomes to create a quality reference

Hello,

I have about 950 million reads from an RNA-Seq data set that covers many developmental time-points. Assembling all the reads doesn't really work because I reach a point where errors are...
Forum: RNA Sequencing 12-15-2016, 08:32 AM
Replies: 0
Views: 707
Posted By dacotahm
Any advanced CummeRbund tutorials out there?

Any advanced CummeRbund tutorials out there? I've only found tutorials that cover the basics in the manual. I'm looking for something more detailed that allows you to manipulate the graphical and...
Forum: RNA Sequencing 12-06-2016, 11:30 AM
Replies: 1
Views: 910
Posted By dacotahm
Just to add more detail, the manual section 9.4...

Just to add more detail, the manual section 9.4 (page 39) shows how the clustering is organized. Is there a way to filter and plot only the reads for a specific cluster?
...
Forum: RNA Sequencing 12-05-2016, 01:09 PM
Replies: 1
Views: 910
Posted By dacotahm
CummeRbund - show individual k-means cluster plots

I'm using CummeRbund to visualize some RNA-Seq data. I can show expression patterns with this:

ic9 <- csCluster(sigGenes, k=9)
icp9 <- csClusterPlot(ic9)
icp9

...but that shows all 9...
Forum: General 11-28-2016, 09:10 AM
Replies: 0
Views: 1,053
Posted By dacotahm
Comparative Genomics - Make phylogenetic tree of species with available NCBI genomes

Hello,

I'm doing some comparative genomics and NCBI's taxonomy browser is useful for screening species with genomes available. I want to export this in Newick or some standard format so I can...
Forum: Bioinformatics 02-26-2016, 09:23 AM
Replies: 2
Views: 602
Posted By dacotahm
What is the best/easiest way to apply annotation info to a fasta defline?

I've been doing some de novo transcriptome work and using standalone BLAST and other programs to identify gene homologs, features, etc. and I would like to know what the best way to add some of this...
Forum: Bioinformatics 04-14-2013, 08:58 AM
Replies: 2
Views: 726
Posted By dacotahm
How? - Apply BLAST identities to transcriptome

Hello, I could use help with the following problem -

I've assembled a transcriptome and I can BLAST against Drosophila to identify some of the transcripts. Now I have two files: the BLAST output...
Forum: Bioinformatics 02-13-2013, 07:58 AM
Replies: 1
Views: 625
Posted By dacotahm
How do you pull a bunch of reads by ID?

Here's what I'm trying to do-

I'm trying to assemble a couple a candidate genes from a pool of illumina reads. I have a species close to drosophila and would like to align 60 million reads to a...
Forum: Bioinformatics 12-10-2012, 04:43 PM
Replies: 10
Views: 839
Posted By dacotahm
Hm....it worked when I copied a fragment into a...

Hm....it worked when I copied a fragment into a new text file using nano but not when I saved the same fragment into a plain text with gedit or kate...

But I think I may have it- thank you for...
Forum: Bioinformatics 12-10-2012, 04:37 PM
Replies: 10
Views: 839
Posted By dacotahm
I copied it right out of my terminal into Kate...

I copied it right out of my terminal into Kate and saved it as plain text. I did change the input.close() to inputFile.close(). It still returns the same error.
Forum: Bioinformatics 12-10-2012, 04:25 PM
Replies: 10
Views: 839
Posted By dacotahm
I saw the seperator was a comma, ...I wasn't sure...

I saw the seperator was a comma, ...I wasn't sure what it was choking on so I ran it on just this fragment and got the same error:

5,b,787
6,b,493
7,b,1344
8,b,906
9,b,960
10,b,544
11,b,4109...
Forum: Bioinformatics 12-10-2012, 04:18 PM
Replies: 10
Views: 839
Posted By dacotahm
Thanks for the response- I'm getting this error...

Thanks for the response- I'm getting this error when I run it on my data:

Traceback (most recent call last):

File "frequency.py", line 5, in <module>

curLength =...
Forum: Bioinformatics 12-10-2012, 12:49 PM
Replies: 10
Views: 839
Posted By dacotahm
Transcript length/frequncy plot

I've created a few different assemblies, and I'd like to make a dotplot of the number of transcripts at a certain length. I'm using R or python. Right now I've got to the point where my data looks...
Forum: Bioinformatics 04-27-2012, 09:51 AM
Replies: 0
Views: 1,505
Posted By dacotahm
Standalone BLAST output format question

I'm using stand-alone BLAST to align transcripts I've assembled of a non-model species to the drosophila transcriptome. I want my output to be a CSV file that includes the actual NAME of the gene. ...
Forum: Bioinformatics 11-22-2011, 02:13 PM
Replies: 1
Views: 1,027
Posted By dacotahm
How can I estimate overall coverage against a reference database?

I'm doing de novo assembly on RNA-seq data and I do a stand-alone BLAST against a reference transcriptome. I want to know how much of my assembly aligned, preferably as a percentage so I can...
Forum: Bioinformatics 10-10-2011, 10:08 AM
Replies: 0
Views: 1,400
Posted By dacotahm
Velvet-Oases Memory Problem

I'm using a small data set to test Velvet-Oases of about a million (av. length 200bp) reads. Pretty soon we're going to get a much larger data set, but the memory requirements for the much smaller...
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