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Search took 0.03 seconds. Search: Posts Made By: thh32
Forum: Bioinformatics 01-15-2016, 08:16 AM
Replies: 0
Views: 2,666
Posted By thh32
How to get SNP abundance from a metagenomic VCF?

So I have a VCF:...
Forum: Bioinformatics 03-09-2015, 11:07 AM
Replies: 5
Views: 1,704
Posted By thh32
We have access to 500Gb RAM and we are aligning...

We have access to 500Gb RAM and we are aligning nucleotide sequences to Swissprot. hmmm ok I will have a look at that. I also found Swipe which provides e values so I am giving it a try.
Forum: Bioinformatics 03-09-2015, 08:25 AM
Replies: 5
Views: 1,704
Posted By thh32
Straight forward Smith waterman aligner?

So I am looking for a straight forward smith waterman program which hasnt been "enhanced" and just accepts fasta files and compares to find common parts. The reason for not wanted enhanced versions...
Forum: Bioinformatics 02-12-2015, 09:01 AM
Replies: 15
Views: 3,459
Posted By thh32
We are trying to provide functional annotation to...

We are trying to provide functional annotation to an assembly we have recently created. We are using 1 core per blast job as to allow as many as possible to get onto the server at once.
Forum: Bioinformatics 02-12-2015, 07:26 AM
Replies: 15
Views: 3,459
Posted By thh32
Each of the query files is ~9Mb as the original...

Each of the query files is ~9Mb as the original file of 6.5Gb was split into 1000 smaller pieces to speed up the process however the bacteria subset of Trembl is 30Gb which seems to be the issue but...
Forum: Bioinformatics 02-12-2015, 07:22 AM
Replies: 15
Views: 3,459
Posted By thh32
Yes this is my issue, just looked at the cost and...

Yes this is my issue, just looked at the cost and its going to be better to buy a whole load of new nodes for our Uni HPC instead.
Forum: Bioinformatics 02-12-2015, 07:00 AM
Replies: 15
Views: 3,459
Posted By thh32
We are currently blasting against Swiss prot and...

We are currently blasting against Swiss prot and the trembl sections specific for bactieria and archaea. Also yes I was hoping I could disciss prices with them but the free 750 hours you get per...
Forum: Bioinformatics 02-12-2015, 05:43 AM
Replies: 15
Views: 3,459
Posted By thh32
Experiences using cloud computing?

So I am currently considering using a cloud computing service as I have 180,000 blast jobs that need doing and to do that on our Uni servers would take a few months. Each job will take ~30 hours and...
Forum: Bioinformatics 12-18-2014, 05:41 AM
Replies: 2
Views: 3,953
Posted By thh32
Convert sam file to fasta file.

Is there a way to convert a sam file into a fasta file?
Forum: Bioinformatics 11-26-2014, 01:51 AM
Replies: 3
Views: 8,606
Posted By thh32
Same issue here, ever find out a solution?

Same issue here, ever find out a solution?
Forum: Bioinformatics 11-19-2014, 08:08 AM
Replies: 2
Views: 1,102
Posted By thh32
Help creating phylogenetic map

I currently have a list of taxonID's which I have obtained by blast identification of the contigs within my metagenomic assembly. I have tried using Phylot to create a tree and then iTOL to display...
Forum: Bioinformatics 11-17-2014, 06:10 AM
Replies: 3
Views: 2,278
Posted By thh32
No we dont from what I know and thanks, I had a...

No we dont from what I know and thanks, I had a google around before posting and saw a few others have had the same issue and as you say with that thread, no resolution had been found.
Forum: Bioinformatics 11-17-2014, 03:59 AM
Replies: 3
Views: 2,278
Posted By thh32
Velvet maximum element with 32bit error

So I have been running velvet on a metagenomic dataset (35Gb flash joined) using 51 Kmer and it failed with the error:

[888200.245154] >>> Reached maximum elements addressable with 32 bits...
Forum: Bioinformatics 10-27-2014, 08:07 AM
Replies: 2
Views: 897
Posted By thh32
There is no specirfic tool. I have been looking...

There is no specirfic tool. I have been looking for a program that will do the same on metagenomic data but had to write a load of code myself to try and work around the issues. May I ask is your...
Forum: Bioinformatics 10-22-2014, 04:29 AM
Replies: 0
Views: 1,015
Posted By thh32
HUGE differences between multiple sequence aligners.

So I have 2000 sequences I am aligning to identify comonalities. Firstly I am using different MSA programs (clustalo, muscle and MAFFT) and then converting them to a hmmprofile so I can view using...
Forum: Bioinformatics 10-21-2014, 05:09 AM
Replies: 3
Views: 1,143
Posted By thh32
The sequences have had any duplicates removed and...

The sequences have had any duplicates removed and they are a short region which occur in a defence mechanism in bacteria but we were wondering if they have any similarity to each other. I figured it...
Forum: Bioinformatics 10-21-2014, 04:14 AM
Replies: 3
Views: 1,143
Posted By thh32
MSA with 80,000 30bp seqences, provides 1500 base in output file

I have been trying to do a multiple sequence alignment with 80,000 sequences to identify any similarities. All bases are 36-37bp long however when I run the multiple sequence alignment (tried...
Forum: Bioinformatics 10-20-2014, 08:56 AM
Replies: 0
Views: 1,055
Posted By thh32
Compare 10000 sequences in hmmer

So I have used Clustal Omega to do a multiple alignment and hmmbuild to create a hmmer profile for 10000 copies of the same repeat region (30bp long) however when the output is viewed as a hmm logo...
Forum: Bioinformatics 10-16-2014, 05:06 AM
Replies: 0
Views: 1,332
Posted By thh32
Code for identifying and renaming contigs

Just completed an assembly and was wondering if there is any code around which will take my assembly, blast it, get the best hits and rename the contigs to the species they are?
Forum: Bioinformatics 10-16-2014, 02:18 AM
Replies: 1
Views: 1,152
Posted By thh32
Bowtie stopped half way through

So running a bowtie job on the cluster and was wondering if there is a way to get it to continue from where it stopped or do I just have to start all over again?
Forum: Bioinformatics 10-16-2014, 02:16 AM
Replies: 2
Views: 897
Posted By thh32
Surely you should assemble the data, identify and...

Surely you should assemble the data, identify and viral DNA by blasting your contigs. Look for contigs with both viral and bacterial DNA. Ensure it isnt just a single bacterial gene in a viral genome...
Forum: Bioinformatics 10-13-2014, 04:37 AM
Replies: 1
Views: 1,376
Posted By thh32
Searching for protein in fasta file

So I have protein (cas1) I want to look for in a bunch of fasta files and Pfam has a 'HMM logo' for the protein (http://pfam.xfam.org/family/PF01867#tabview=tab4). I was wondering if it is possible...
Forum: Bioinformatics 09-22-2014, 03:56 AM
Replies: 0
Views: 1,587
Posted By thh32
Limits of Crass?

Hi I am about to start using Crass: the CRISPR assembler, to produce CRISPR regions from 1Tb of metagneomic data. I was wondering if anyone knows the limitations of this program? Is it RAM hungry?...
Forum: Bioinformatics 09-08-2014, 04:06 PM
Replies: 4
Views: 3,095
Posted By thh32
This would work if I wanted a SAM file output but...

This would work if I wanted a SAM file output but I am aiming for a similar output to that provided with bowtie where you get a file of the reads that align to the indexed file and a seperate file...
Forum: Bioinformatics 09-08-2014, 12:03 PM
Replies: 4
Views: 3,095
Posted By thh32
No BWA alignment output files!

Hi,

I have been using Bowtie for the last few months for alignment but now have a file for indexing which is 6Gb and Bowtie cannot deal with so I have moved onto using BWA, the indexing went fine...
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