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Forum: Bioinformatics 12-08-2018, 07:33 AM
Replies: 6
Views: 1,031
Posted By ctseto
In WSL, apt-get install qiime is QIIME 1.9.0 I...

In WSL, apt-get install qiime is QIIME 1.9.0
I installed miniconda, then used the linux tutorial from the qiime2.org page.
You need Xming on your Win10 machine and a reasonably new version of Win10...
Forum: Bioinformatics 12-07-2018, 04:23 AM
Replies: 1
Views: 445
Posted By ctseto
Annotation may reveal what's not there, esp if...

Annotation may reveal what's not there, esp if you know from exp that a given gene is present (eg someone PCR/subcloned ). Guessing eukaryote and that you may have hit some contigs that are repeat...
Forum: Bioinformatics 12-06-2018, 06:23 AM
Replies: 6
Views: 1,031
Posted By ctseto
Windows Subsystem for Linux

New job, desk includes a workstation with windows10. I've got WSL running for silly things like small qiime jobs, but wondering if anyone else is doing anything with WSL asides from replacing PuTTy...
Forum: De novo discovery 12-06-2018, 06:03 AM
Replies: 0
Views: 1,852
Posted By ctseto
Thoughts on combining PE runs to improve assemblies?

Have little experience with metagenomes vs genomes, so this post is probably full of stupid questions. My thinking is to do a first pass assembly, map reads to the scaffolds and directly assess the...
Forum: Bioinformatics 12-06-2018, 05:55 AM
Replies: 8
Views: 9,653
Posted By ctseto
Haven't seen any as of late 2018, and I've been...

Haven't seen any as of late 2018, and I've been looking after getting back into de novo assembly...
Always possible that as someone getting back in that I've missed something.

Edit: I see megahit...
Forum: Bioinformatics 05-22-2014, 06:46 AM
Replies: 3
Views: 825
Posted By ctseto
What's the insert size distribution for the reads...

What's the insert size distribution for the reads at the ends? If the insert size is equal to the length of the contig, it would be the ends pairing with each other across a rolling circle, perhaps.
Forum: De novo discovery 05-09-2014, 11:35 AM
Replies: 3
Views: 3,124
Posted By ctseto
By its nature, SAM has the alignment in it...

By its nature, SAM has the alignment in it (SAM=Sequence Alignment Map).

First: Did you sort your SAM file? (will need samtools for this).

Checking the manual again, it looks like it should be:...
Forum: De novo discovery 04-07-2014, 01:28 PM
Replies: 2
Views: 2,248
Posted By ctseto
"I'm assembling some bacterial genomes for which...

"I'm assembling some bacterial genomes for which there are no close reference sequences available"

In the absence of reference data to align your contigs against (plasmids, EST tags, mRNA), you...
Forum: Introductions 03-26-2014, 12:13 PM
Replies: 6
Views: 2,022
Posted By ctseto
I'm looking at NCBI's list of 25712 EST's for H....

I'm looking at NCBI's list of 25712 EST's for H. lupulus and they are somewhat short, in the <1k range. It's probable there are repeats in the hop genome that your assembly would stall on.
...
Forum: Introductions 03-26-2014, 11:45 AM
Replies: 6
Views: 2,022
Posted By ctseto
There are some interesting new de novo assembly...

There are some interesting new de novo assembly papers on the polyploid loblolly pine that might give you some ideas.

http://genomebiology.com/content/pdf/gb-2014-15-3-r59.pdf...
Forum: Bioinformatics 03-13-2014, 06:48 AM
Replies: 4
Views: 1,570
Posted By ctseto
1. Combine the reads together, especially with...

1. Combine the reads together, especially with that much overlap. Use FLASH, though I think Pandaseq does the same.

2. Depends on how much of your reads are unique. If a lot of your read content...
Forum: De novo discovery 03-03-2014, 07:31 AM
Replies: 1
Views: 2,243
Posted By ctseto
Zerbino tells us there shouldn't be any...

Zerbino tells us there shouldn't be any difference, but what you've found is interesting.

Have you tried this without the singletons and just the paired reads?

It's interesting that your -long...
Forum: Bioinformatics 02-16-2014, 03:48 PM
Replies: 11
Views: 1,670
Posted By ctseto
Is it repetitive? Polyploid? Have you done a...

Is it repetitive? Polyploid? Have you done a dotplot of your organism against the other related reference?
Forum: Bioinformatics 02-07-2014, 11:40 AM
Replies: 4
Views: 1,945
Posted By ctseto
From the velvet manual:

From the velvet manual:
Forum: De novo discovery 01-27-2014, 05:49 AM
Replies: 5
Views: 2,020
Posted By ctseto
Search google for "illumina adapter letter" ...

Search google for "illumina adapter letter"

http://support.illumina.com/downloads/illumina_adapter_sequences_letter.ilmn

Depending on what you are running, check and see if the adapters used in...
Forum: Bioinformatics 01-23-2014, 03:05 PM
Replies: 3
Views: 1,176
Posted By ctseto
BLAST would be online (through NCBI) for single...

BLAST would be online (through NCBI) for single fastas, or downloading and compiling blast on your end along with the database, and running a search of your contigs against the database.

Curious...
Forum: Bioinformatics 01-17-2014, 07:23 AM
Replies: 15
Views: 5,007
Posted By ctseto
Diginorm may also help with memory requirements,...

Diginorm may also help with memory requirements, though I haven't run benchmarks recently.
Forum: General 12-18-2013, 04:47 AM
Replies: 6
Views: 7,746
Posted By ctseto
There's a NEB kit that removes human DNA for...

There's a NEB kit that removes human DNA for microbiome workflows; NEB has a protocol to elute the human DNA.

https://www.neb.com/products/e2612-nebnext-microbiome-dna-enrichment-kit
...
Forum: De novo discovery 12-13-2013, 06:15 AM
Replies: 10
Views: 7,377
Posted By ctseto
I've had pretty good results using SPAdes....

I've had pretty good results using SPAdes. Comparing my velvet runs against SPAdes from common files is pretty night and day.

An additional long-insert library might be helpful, especially if...
Forum: Metagenomics 12-13-2013, 06:13 AM
Replies: 7
Views: 8,643
Posted By ctseto
Also worth noting that qiime is now at version...

Also worth noting that qiime is now at version 1.8.0. I'll be giving it a go soon...
Forum: Bioinformatics 12-03-2013, 11:12 AM
Replies: 8
Views: 5,226
Posted By ctseto
Google for "Velvet Columbus", which is the...

Google for "Velvet Columbus", which is the reference-guided de novo assembly pipeline.

(Though on the off-chance you get weird results)

http://bioweb2.pasteur.fr/docs/velvet/Columbus_manual.pdf
Forum: Bioinformatics 11-20-2013, 01:18 PM
Replies: 13
Views: 2,878
Posted By ctseto
Fair enough. I'm sure you're aware of NCBI's...

Fair enough. I'm sure you're aware of NCBI's Viral Genomes Resource; it might be a good place to check for reference genomes if you haven't done so already. In the bacteria/eukaryote world there are...
Forum: Bioinformatics 11-20-2013, 08:22 AM
Replies: 13
Views: 2,878
Posted By ctseto
1. Mapping single-end gives you greater...

1. Mapping single-end gives you greater flexibility in forcing maps; but generally paired end maps would be considered more reliable, since to map two reads both reads must meet the conditions...
Forum: Bioinformatics 11-20-2013, 03:52 AM
Replies: 5
Views: 5,730
Posted By ctseto
What happens when you use --local...

What happens when you use --local --very-sensitive-local at the same time? I assume it picks one and keeps on going?
Forum: Bioinformatics 11-20-2013, 03:43 AM
Replies: 13
Views: 2,878
Posted By ctseto
Your n50 is low and your max contig is 2332. ...

Your n50 is low and your max contig is 2332.

Perhaps try mapping just to your largest contig to assess coverage for now?

Also, are you running MetaVelvet downstream of this?
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