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Search: Posts Made By: Mithril
Forum: Bioinformatics 10-16-2012, 07:51 AM
Replies: 0
Views: 1,848
Posted By Mithril
Calculate core and Pan genome of bacteria

Hey all,
can sombody tell me how to go pull out the core genome and pan genomes between different strains of bacteria? Are there any tools to do this? i have read about bi directional blast being...
Forum: Bioinformatics 10-11-2012, 09:23 PM
Replies: 4
Views: 1,626
Posted By Mithril
Thank you jimmybee! MetaPhlAn looks good. ...

Thank you jimmybee! MetaPhlAn looks good.

Any more recommendations?

Once again, thank you for all your solutions.
Forum: Bioinformatics 10-11-2012, 06:21 AM
Replies: 4
Views: 1,626
Posted By Mithril
Thank you for you suggestion. Yes, I have. I...

Thank you for you suggestion.

Yes, I have. I would really like something that has a lot of standalone capacity instead of a webserver....
Forum: Bioinformatics 10-11-2012, 12:12 AM
Replies: 4
Views: 1,626
Posted By Mithril
Classify Bacterial and Archaeal fragments from 454-Metagenome

Hello all,
I have just started working with 454 metagenome datasets and was wondering if there is any tool that can classify reads from 454 into bacterial or archaeal sequences?

I have come...
Forum: Metagenomics 08-19-2012, 10:26 PM
Replies: 3
Views: 3,892
Posted By Mithril
Thank you for the tool, ill check it out!

Thank you for the tool, ill check it out!
Forum: Metagenomics 08-13-2012, 01:40 AM
Replies: 3
Views: 3,892
Posted By Mithril
Tool to identify 16s rRNA fragments in raw data

Hello,
I have metagenome data samples in FASTA format downloaded from EBI and CAMERA. I wanted to extract 16s rRNA fragments from this FASTA file. Can anybody tell me how exactly to go about doing...
Forum: Bioinformatics 04-21-2012, 11:46 AM
Replies: 8
Views: 2,706
Posted By Mithril
Thank you for the TRF link, In an earlier...

Thank you for the TRF link,

In an earlier post you had mentioned that you did have a tool to find reads in nextgen alignment but may not work for 454, would it be possible for me to use the tool...
Forum: Bioinformatics 04-21-2012, 11:30 AM
Replies: 8
Views: 2,706
Posted By Mithril
Oww.. Alright I will run the data through TRF,...

Oww.. Alright I will run the data through TRF, would it be possible for you to link me to the tool that you are talking about?
Forum: Bioinformatics 04-21-2012, 10:59 AM
Replies: 8
Views: 2,706
Posted By Mithril
Well, I got 454 reads from 2 seperate genotypes....

Well, I got 454 reads from 2 seperate genotypes. They were assembled and annotated. Now I want to generate SSRs that are polymorphic between the two assemblies. MISA is generally used to detect SSRs...
Forum: Bioinformatics 04-21-2012, 07:35 AM
Replies: 8
Views: 2,706
Posted By Mithril
Detect polymorphic SSRs between two assemblies

Hello all,
I have generated two assemblies from two separate genotypes. Is there a tool to search for polymorphic SSRs between these two assemblies?
Forum: Bioinformatics 04-13-2012, 07:46 AM
Replies: 3
Views: 1,357
Posted By Mithril
Ow... My bad. i just realised my mistake. thank...

Ow... My bad. i just realised my mistake. thank you
Forum: Bioinformatics 04-13-2012, 07:23 AM
Replies: 3
Views: 1,357
Posted By Mithril
SNP detection by samtools returns dots under the reference columns

Hello,
I have a very peculiar problem. I used samtools to get SNPs using the mpileup command. The commands that i used are as follows:

samtools mpileup -uf...
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