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Search: Posts Made By: Gorbenzer
Forum: Illumina/Solexa 05-11-2015, 02:17 AM
Replies: 10
Views: 3,817
Posted By Gorbenzer
Thanks, i'll give a look at it!

Thanks, i'll give a look at it!
Forum: Illumina/Solexa 05-07-2015, 03:10 AM
Replies: 10
Views: 3,817
Posted By Gorbenzer
In fact, we would like to use alternative...

In fact, we would like to use alternative reagents for library preparation (bacterial genomes/metagenomes, 16S rRNA profiling and RnaSeq). Do you know any MiSeq-compatible kit?
Forum: Illumina/Solexa 05-06-2015, 03:14 AM
Replies: 10
Views: 3,817
Posted By Gorbenzer
Lightbulb MiSeq alternative/cheaper regents

Hi guys,
we own a MiSeq that we use quite a lot and we are now looking for alternative reagents to reduce cots.
There are non-illumina flowcells on sale?
Anyone use alternative reagents or dilute...
Forum: Bioinformatics 05-27-2014, 09:53 AM
Replies: 2
Views: 1,658
Posted By Gorbenzer
up! anyone have suggestions?

up! anyone have suggestions?
Forum: Bioinformatics 05-26-2014, 09:29 AM
Replies: 2
Views: 1,658
Posted By Gorbenzer
metagenomics contigs taxonomy assignment

Hi everyone,
i'm doing metagenomic assemblies of environmental samples rich in one species (>50% of the bacterial content is coming from a single species).

I got a good amount of contigs using...
Forum: Bioinformatics 03-24-2014, 11:48 AM
Replies: 1
Views: 1,657
Posted By Gorbenzer
co-occurrence analysis guide / software

Dear all,
i'm looking for a guide / software for co-occurrence and co-exclusion analysis of 16S profiling tabular data and RnaSeq/Microarray expression tabular data.

Anyone have any suggestion?
...
Forum: Bioinformatics 03-24-2014, 11:07 AM
Replies: 3
Views: 1,006
Posted By Gorbenzer
It's me who started the post on MIRA mailing...

It's me who started the post on MIRA mailing list.

We've done some testing and comparison with fully assembled genomes.

MIRA 4 gives more contigs but avoids assembly errors. We'll stick with...
Forum: Bioinformatics 03-20-2014, 08:24 AM
Replies: 3
Views: 1,006
Posted By Gorbenzer
MIRA 4 poor performance compared to 3.9.X

Dear all,
i'm having big issues using MIRA 4 for bacterial denovo sequencing: number of contigs generated by assembly with MIRA 4 is insanely higher than with MIRA 3.9.X.

Here are some comparison...
Forum: Bioinformatics 03-20-2014, 02:35 AM
Replies: 0
Views: 758
Posted By Gorbenzer
Contig Overlap discovery/alignment

Dear all,
i've been using Lasergene SeqMan for discovery of overlaps between assembled contigs but i'n not fully satisfied with it.

Anyone have any suggestion about software for contigs overlap...
Forum: Bioinformatics 02-10-2014, 03:04 AM
Replies: 2
Views: 1,045
Posted By Gorbenzer
set allowed when aligning with BWA

Hi everyone,
i've been using BWA-mem for RnaSeq and i'd like to use this tool in order to find genes in public metagenomic datasets that are homolog to my gene pool.

There's a way to increase the...
Forum: Ion Torrent 01-29-2014, 08:31 AM
Replies: 0
Views: 1,294
Posted By Gorbenzer
Exclamation Bacteria transcriptomics RnaSeq - low output

Hi everyone,
we are testing the v2 RnaSeq kit for IonTorrent in order to do some bacteria transcriptomics.

During library preparations all quality values seems good but when we sequence the...
Forum: Ion Torrent 01-29-2014, 08:12 AM
Replies: 14
Views: 7,473
Posted By Gorbenzer
Hi guys, we have trying to use v2 kits for...

Hi guys, we have trying to use v2 kits for Bacterial transcriptimics. All values during library preparation seems good but final output is really low, with 50/60% of polyclonals. It seems that the...
Forum: Bioinformatics 12-13-2013, 08:21 AM
Replies: 0
Views: 1,754
Posted By Gorbenzer
modify a genbank file through vcf file infrmations

Dear all,
i'd like to include the information from a vcf file generated by VarScan (insertion, deletions and substitutions) in my genbank file.

For example if the vcf file says that a C should be...
Forum: Bioinformatics 10-30-2013, 04:02 AM
Replies: 0
Views: 1,352
Posted By Gorbenzer
Arrow RnaSeq differential expression

Hi everyone,
It's time to use our IonTorrent to evaluate difference in trascription when our bacteria are grown in different conditions.

Wiki...
Forum: RNA Sequencing 05-08-2013, 01:17 AM
Replies: 1
Views: 1,895
Posted By Gorbenzer
Thx so much! we are going to try RNA-seq with our...

Thx so much! we are going to try RNA-seq with our PGM too!
Forum: RNA Sequencing 05-03-2013, 03:17 AM
Replies: 7
Views: 6,352
Posted By Gorbenzer
Thanks so much, i'll read those in the week...

Thanks so much,
i'll read those in the week end!!
Forum: RNA Sequencing 05-03-2013, 02:32 AM
Replies: 7
Views: 6,352
Posted By Gorbenzer
Thanks, i'll try it! Do you know any...

Thanks, i'll try it!

Do you know any paper/review to be used as a first-time guide to RNA-seq? :)

EDIT: you mentioned splicing, i'm going to analyze only bacterial data, so no splicing, can i...
Forum: Metagenomics 04-24-2013, 01:08 AM
Replies: 4
Views: 3,465
Posted By Gorbenzer
Thanks for the reply, usually we design 200bp...

Thanks for the reply,
usually we design 200bp specific primers but this time we have to amplify the fungal ITS region that is around 400/450 bp so primers can't be designed inside the variable...
Forum: Metagenomics 04-22-2013, 08:42 AM
Replies: 4
Views: 3,465
Posted By Gorbenzer
fungal ITS profiling primers and 500bp Ion Torrent amplicon sequencing

Hi everyone,
i'm going to try ITS profiling using the primers developed here ( http://www.plosone.org/article/info:doi/10.1371/journal.pone.0040863 ) but the amplicon is ~500bp (470bp plus bacrcode...
Forum: Metagenomics 04-22-2013, 02:35 AM
Replies: 0
Views: 1,778
Posted By Gorbenzer
please delete, moved to ITS profiling

please delete, moved to ITS profiling
Forum: Metagenomics 04-22-2013, 02:25 AM
Replies: 6
Views: 3,416
Posted By Gorbenzer
thx so much! i'll try to get started with this...

thx so much! i'll try to get started with this software :)
Forum: RNA Sequencing 04-19-2013, 07:15 AM
Replies: 7
Views: 6,352
Posted By Gorbenzer
softwares for bacterial RNA-Seq analysis?

Hi everyone,
in our lab we are going to try to do some bacterial RNA-Seq run with our Ion Torrent.

Anyone with experience in Bacterial RNA-Seq that can suggest the best softwares to analyze the...
Forum: Metagenomics 04-19-2013, 07:03 AM
Replies: 6
Views: 3,416
Posted By Gorbenzer
Local would be great, we have two servers for our...

Local would be great, we have two servers for our analysis.

I'd like to try all the different approaces:
- Try to assembly all the data to see if i can get draft genomes of a few highly present...
Forum: Metagenomics 04-19-2013, 05:47 AM
Replies: 6
Views: 3,416
Posted By Gorbenzer
Thanks for the reply, metAMOS pipeline i think...

Thanks for the reply, metAMOS pipeline i think it's worth a try, any other suite/pipeline or tools for analyze gene composition??
Forum: Metagenomics 04-19-2013, 02:57 AM
Replies: 6
Views: 3,416
Posted By Gorbenzer
survery: what assembler, gene prediction and gene annotation softwares do you use?

Hi everyone,
i'm going to analize some Ion Torrent metagenomic data and have read a lot of posts about different softwares but i have very limited time and can't decide what one to try first.
...
Showing results 1 to 25 of 45

 


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