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Search: Posts Made By: cliffbeall
Forum: Bioinformatics 12-19-2017, 07:22 AM
Replies: 19
Views: 2,741
Posted By cliffbeall
Sorry, late to the party here but I was googling...

Sorry, late to the party here but I was googling the error:
BLAST Database error: BLASTDB alias file creation failed. Some referenced files may be missing
trying to restrict blastn searches of...
Forum: Academic/Non-Profit Jobs 08-03-2017, 07:33 AM
Replies: 0
Views: 788
Posted By cliffbeall
Research Associate Oral Microbiome Informatics Columbus, Ohio

Research Associate in Bioinformatics of the Oral Microbiome, Ohio State University

The laboratory of Drs. Eugene Leys and Ann Griffen in the Division of Biosciences, College of Dentistry at the...
Forum: Bioinformatics 03-02-2017, 05:28 AM
Replies: 3
Views: 1,730
Posted By cliffbeall
Since this is one of the top hits while googling,...

Since this is one of the top hits while googling, thought I would leave here that CheckM with the tetra_pca command will do this:

https://github.com/Ecogenomics/CheckM/wiki/Plots
Forum: Bioinformatics 02-15-2017, 07:06 AM
Replies: 4
Views: 1,167
Posted By cliffbeall
There is a EMBOSS program ABIview...

There is a EMBOSS program ABIview (http://emboss.toulouse.inra.fr/cgi-bin/emboss/help/abiview) although that seems to just output fasta format.

Maybe 4peaks with Applescript? Or is there an...
Forum: Bioinformatics 08-02-2016, 01:18 PM
Replies: 1
Views: 1,798
Posted By cliffbeall
The manual says rma is a binary compressed format...

The manual says rma is a binary compressed format - it didn't seem to be recognized by zip, gzip or bzip2 for me although maybe I was doing something wrong.

The latest MEGAN includes a...
Forum: Bioinformatics 05-03-2016, 11:04 AM
Replies: 2
Views: 1,292
Posted By cliffbeall
The NCBI database is only from named, cultured,...

The NCBI database is only from named, cultured, species so it will be missing sequences for the large diversity of uncultured organisms. Its probably not useful for a high throughput survey...
Forum: Bioinformatics 04-27-2016, 01:37 PM
Replies: 3
Views: 1,156
Posted By cliffbeall
Sorry, I missed that you had a specific list of...

Sorry, I missed that you had a specific list of strains - I think you can find the genome accessions in this table so you know which folders to look at:
...
Forum: Bioinformatics 04-27-2016, 09:52 AM
Replies: 3
Views: 1,156
Posted By cliffbeall
They are in NCBI, at least where I get bacterial...

They are in NCBI, at least where I get bacterial genomes (which changed recently).

In the subfolders of this directory: NCBI Helicobacter genomes...
Forum: Bioinformatics 04-27-2016, 09:27 AM
Replies: 2
Views: 1,851
Posted By cliffbeall
It looks like your sequence is in fasta format, I...

It looks like your sequence is in fasta format, I think you need to get them into Phylip format for RAxML. I do that with Mesquite on the Mac, biopython alignIO will also work.
Forum: Illumina/Solexa 04-27-2016, 09:19 AM
Replies: 6
Views: 1,579
Posted By cliffbeall
Illumina sequencing doesn't work well on...

Illumina sequencing doesn't work well on fragments over ~1000 bp because the cluster amplification is less efficient for longer pieces. You can use a Covaris, BioRupter or something similar to reduce...
Forum: Bioinformatics 04-27-2016, 09:06 AM
Replies: 5
Views: 3,362
Posted By cliffbeall
Thread necromancy

bowtie2build gave me a segmentation fault similar to the above, it turned out the fasta file was corrupted. It actually went a bit further in the process, generating a bunch of index files.

You...
Forum: General 11-17-2015, 01:14 PM
Replies: 9
Views: 2,328
Posted By cliffbeall
SNPsaurus, could you share that protocol? We do...

SNPsaurus, could you share that protocol? We do know the sequence of host and bacteria so it should be possible to do that in either direction.
Forum: General 11-17-2015, 12:50 PM
Replies: 9
Views: 2,328
Posted By cliffbeall
We have seen something kind of similar with a...

We have seen something kind of similar with a bacteria - invertebrate infection system. The bacterial reads are a small percentage, even though they can kill off the hosts.

We're working on...
Forum: Bioinformatics 10-06-2015, 10:10 AM
Replies: 5
Views: 1,714
Posted By cliffbeall
You might want to try comparing at the protein...

You might want to try comparing at the protein level to the nr protein database and/or kmer frequency analysis, since I'm not sure how much bacteria from soil will match at the nucleotide level to...
Forum: Bioinformatics 09-17-2015, 05:36 AM
Replies: 18
Views: 13,108
Posted By cliffbeall
I am fairly sure fr-firststrand means read one...

I am fairly sure fr-firststrand means read one (aka forward read or fr) corresponds to the reference genome sequence (firststrand). fr-secondstrand means read one corresponds to the reverse...
Forum: Bioinformatics 09-14-2015, 10:10 AM
Replies: 18
Views: 13,108
Posted By cliffbeall
The two genes are on different strands, you can...

The two genes are on different strands, you can see by the little chevrons in the annotation track at bottom, so that is expected.
Forum: Bioinformatics 09-10-2015, 11:24 AM
Replies: 2
Views: 1,254
Posted By cliffbeall
I did something like this recently and about 40%...

I did something like this recently and about 40% of genes did not get a COG assignment. One way to evaluate the quality would be to check for a list of core housekeeping genes to make sure they are...
Forum: Bioinformatics 07-29-2015, 05:26 AM
Replies: 2
Views: 967
Posted By cliffbeall
I just ran into this (on BioLinux). With...

I just ran into this (on BioLinux). With administrator privileges, you can type:

sudo ln -s /usr/bin/show-coords /usr/local/bin/show-coords

and minimus2 will run.
Forum: Sample Prep / Library Generation 07-21-2015, 08:34 AM
Replies: 5
Views: 2,471
Posted By cliffbeall
Couldn't you add the Illumina adapter bits by...

Couldn't you add the Illumina adapter bits by overlapping PCR, as done in 16S amplicon and Nextera protocols?
Forum: General 06-30-2015, 08:14 AM
Replies: 1
Views: 2,361
Posted By cliffbeall
Paraformaldehyde is the solid form, when its...

Paraformaldehyde is the solid form, when its dissolved in aqueous solution it becomes formaldehyde. Formalin is 37% formaldehyde that is usually sold in solution and from what I read also contains a...
Forum: Bioinformatics 05-29-2015, 05:25 AM
Replies: 1
Views: 1,270
Posted By cliffbeall
Maybe check out snpEff...

Maybe check out snpEff (http://snpeff.sourceforge.net/)?
Forum: Bioinformatics 05-27-2015, 11:25 AM
Replies: 3
Views: 2,214
Posted By cliffbeall
There is a tool on the IMG that generates Genbank...

There is a tool on the IMG that generates Genbank format directly - there is a button at the bottom of the genome main page ("Taxon Details") saying Export Genome Data and Generate Genbank File. It...
Forum: Academic/Non-Profit Jobs 05-21-2015, 01:06 PM
Replies: 0
Views: 876
Posted By cliffbeall
Postdoc in Bioinformatics of the Oral Microbiome, Ohio State University

The laboratory of Drs. Eugene Leys and Ann Griffen in the Division of Biosciences, College of Dentistry at the Ohio State University has an opening for a postdoctoral associate to study the oral...
Forum: Sample Prep / Library Generation 05-18-2015, 06:17 AM
Replies: 11
Views: 3,930
Posted By cliffbeall
We sometimes see amplification of human DNA with...

We sometimes see amplification of human DNA with 16S primers, though not at a very high level. In the cases we have seen it's to a random location that happens to be a (possibly partial) match to the...
Forum: General 05-04-2015, 05:58 AM
Replies: 7
Views: 1,874
Posted By cliffbeall
If I'm peer reviewing a manuscript I try to make...

If I'm peer reviewing a manuscript I try to make sure that there is an accession number. I would urge everyone else to do the same.

It unfortunately seems to be very common to submit the paper...
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