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Search: Posts Made By: pfranchini
Forum: Bioinformatics 02-04-2013, 02:51 AM
Replies: 0
Views: 977
Posted By pfranchini
RAD-tag QTL annotation

Hi,

We are working on a QTL project and we used markers obtained with the RAD method (100 base pair single-end). We built a linkage map and we found some QTLs with both single markers and Interval...
Forum: Sample Prep / Library Generation 09-16-2012, 09:11 AM
Replies: 1
Views: 1,490
Posted By pfranchini
RNA-seq libraries from bird blood

Hi all,
I am planning a RNASeq experiment and I would like to prepare some Illumina libraries. The starting material is avian blood. I had a look around but it is not clear which is the best method...
Forum: Sample Prep / Library Generation 08-08-2011, 01:14 AM
Replies: 5
Views: 2,177
Posted By pfranchini
Hi Conny, I am planning to sequence many...

Hi Conny,

I am planning to sequence many small RNA libraries with an Illumina GA and I have your same questions? Did you receive some feedback?

Thanks in advance

Paolo
Forum: Sample Prep / Library Generation 07-08-2011, 05:48 AM
Replies: 3
Views: 1,221
Posted By pfranchini
mRNAseq, single or paired?

Hi,

We are running a RNA-seq experiment to evaluate differential gene expression in different biological groups using Illumina. We already have some transcriptomic data for this species generated...
Forum: De novo discovery 05-23-2011, 07:00 AM
Replies: 2
Views: 3,381
Posted By pfranchini
Hi, I am planning to generate miRNA data using...

Hi,
I am planning to generate miRNA data using an Illumina GAII and I am a beginner in the miRNA world. Can you please give some detail of your experimental design? My plan is to prepare 10...
Forum: De novo discovery 03-26-2010, 02:02 AM
Replies: 38
Views: 15,031
Posted By pfranchini
We did think about reducing genome with some...

We did think about reducing genome with some techniques like the one you suggested. We are oriented to transcriptome because we just have some sets Illumina short reads about 40 bp of length and we...
Forum: De novo discovery 03-25-2010, 06:10 AM
Replies: 38
Views: 15,031
Posted By pfranchini
Thanks for the info. Actually, we were...

Thanks for the info.

Actually, we were wondering to sequence the transcriptome to obtain a higher coverage and find more SNPs as possible to use them in genotyping and for linkage map studies.
We...
Forum: De novo discovery 03-25-2010, 02:09 AM
Replies: 38
Views: 15,031
Posted By pfranchini
Hi, We are starting a project aiming to detect...

Hi, We are starting a project aiming to detect SNPs in a species without reference genome.
I also have thought to assembly my short reads de novo and use the obtained contigs as reference.
From...
Forum: General 03-01-2010, 11:43 PM
Replies: 0
Views: 1,278
Posted By pfranchini
SNPs discovery with 454

Hi all,

We are interested in a low-budget project based on SNPs detection on trascriptome data of a non model organism using the Roche 454 Titanium system. We have to use a sequencing service and...
Forum: Bioinformatics 09-14-2009, 05:48 AM
Replies: 0
Views: 1,615
Posted By pfranchini
Compare Gene Expression levels

Hi,

I measured the gene expression (RPKM) levels of two groups of animals and I would like to statistically test the differences for each gene.
For example, for genes A, B, C and D I have an...
Forum: Bioinformatics 08-23-2009, 08:20 AM
Replies: 3
Views: 1,424
Posted By pfranchini
I tried TopHat but it seems to give gene...

I tried TopHat but it seems to give gene expression value in RPKM only if a gff3 with known splice junction is supplied and I have not it because I am working with a non-model organism. I am looking...
Forum: Bioinformatics 08-21-2009, 05:54 AM
Replies: 3
Views: 1,424
Posted By pfranchini
gene expression analysys

Hi,
I would like to know if it is available a free software (some commercial ones like CLC and SEQman do it) able to estimate gene expression from a mRNA-seq experiment using as reference to count...
Forum: Bioinformatics 08-10-2009, 06:46 AM
Replies: 2
Views: 2,191
Posted By pfranchini
Thanks, I checked again and bowtie was not in...

Thanks,
I checked again and bowtie was not in the PATH..Now I put it there and TopHat correctly works.

Paolo
Forum: Bioinformatics 07-27-2009, 08:55 AM
Replies: 0
Views: 2,310
Posted By pfranchini
RPKM and TopHat

Hi,
I recently collected a lot of Solexa transcriptome data about different groups of sample of abalone species and I would like to calculate gene expression through RPKM measure. I am working on a...
Forum: Bioinformatics 07-23-2009, 08:25 AM
Replies: 2
Views: 2,191
Posted By pfranchini
TopHat running error

Hi,
I found the same problem of boahua100 while running tophat. I moved the executable files bowtie, bowtie-inspect e bowtie-build in the same path where tophat, the reference file and the reads...
Forum: Bioinformatics 07-15-2009, 08:04 AM
Replies: 1
Views: 1,794
Posted By pfranchini
Unique and repeat Hits

Hi,
In which way I can filter the information of unique and repeat hits of the reads to the reference with Maq? There is a way to obtain a global statistic of the mapping? Thanx

P
Forum: Bioinformatics 07-11-2009, 09:23 AM
Replies: 0
Views: 2,199
Posted By pfranchini
Hash Length

Hi all,
I was trying to align my short reads to reference genomes using different software and settings. I saw that some of them (for example "Mosaik") allow to set the hash lenght (4 - 32) while in...
Forum: Bioinformatics 05-06-2009, 04:11 AM
Replies: 4
Views: 7,234
Posted By pfranchini
Gene Expression through RPKM

Hi all,
I am a new user of the next generation sequencing.
I am working with Illumina output sequence reads of a non-model organism so I have not a reference genome. I would like to quantify gene...
Forum: Introductions 05-06-2009, 02:11 AM
Replies: 0
HI
Views: 1,511
Posted By pfranchini
HI

Hi all,
I am Paolo, italian postdoc working in South Africa.
Nice to hear about you!
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