Forum: Illumina/Solexa
05-11-2015, 02:17 AM
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Replies: 10
Views: 3,948
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Forum: Illumina/Solexa
05-07-2015, 03:10 AM
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Replies: 10
Views: 3,948
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?
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Forum: Illumina/Solexa
05-06-2015, 03:14 AM
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Replies: 10
Views: 3,948
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...
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Forum: Bioinformatics
05-27-2014, 09:53 AM
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Replies: 2
Views: 1,686
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Forum: Bioinformatics
05-26-2014, 09:29 AM
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Replies: 2
Views: 1,686
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...
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Forum: Bioinformatics
03-24-2014, 11:48 AM
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Replies: 1
Views: 1,698
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?
...
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Forum: Bioinformatics
03-24-2014, 11:07 AM
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Replies: 3
Views: 1,019
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...
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Forum: Bioinformatics
03-20-2014, 08:24 AM
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Replies: 3
Views: 1,019
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...
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Forum: Bioinformatics
03-20-2014, 02:35 AM
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Replies: 0
Views: 782
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...
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Forum: Bioinformatics
02-10-2014, 03:04 AM
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Replies: 2
Views: 1,069
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...
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Forum: Ion Torrent
01-29-2014, 08:31 AM
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Replies: 0
Views: 1,305
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...
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Forum: Ion Torrent
01-29-2014, 08:12 AM
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Replies: 14
Views: 7,523
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...
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Forum: Bioinformatics
12-13-2013, 08:21 AM
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Replies: 0
Views: 1,773
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Forum: Bioinformatics
10-30-2013, 04:02 AM
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Replies: 0
Views: 1,378
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...
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Forum: RNA Sequencing
05-08-2013, 01:17 AM
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Replies: 1
Views: 1,926
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Forum: RNA Sequencing
05-03-2013, 03:17 AM
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Replies: 7
Views: 6,389
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Forum: RNA Sequencing
05-03-2013, 02:32 AM
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Replies: 7
Views: 6,389
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...
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Forum: Metagenomics
04-24-2013, 01:08 AM
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Replies: 4
Views: 3,508
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...
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Forum: Metagenomics
04-22-2013, 08:42 AM
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Replies: 4
Views: 3,508
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Forum: Metagenomics
04-22-2013, 02:35 AM
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Replies: 0
Views: 1,792
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Forum: Metagenomics
04-22-2013, 02:25 AM
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Replies: 6
Views: 3,459
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Forum: RNA Sequencing
04-19-2013, 07:15 AM
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Replies: 7
Views: 6,389
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...
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Forum: Metagenomics
04-19-2013, 07:03 AM
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Replies: 6
Views: 3,459
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Forum: Metagenomics
04-19-2013, 05:47 AM
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Replies: 6
Views: 3,459
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Forum: Metagenomics
04-19-2013, 02:57 AM
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Replies: 6
Views: 3,459
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