Forum: Bioinformatics
02-04-2013, 03:51 AM
|
|
Replies: 0
Views: 1,123
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, 10:11 AM
|
|
Replies: 1
Views: 1,713
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, 02:14 AM
|
|
Replies: 5
Views: 2,374
|
|
Forum: Sample Prep / Library Generation
07-08-2011, 06:48 AM
|
|
Replies: 3
Views: 1,395
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, 08:00 AM
|
|
Replies: 2
Views: 3,601
|
|
Forum: De novo discovery
03-26-2010, 03:02 AM
|
|
Replies: 38
Views: 16,835
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, 07:10 AM
|
|
Replies: 38
Views: 16,835
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, 03:09 AM
|
|
Replies: 38
Views: 16,835
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
03-02-2010, 12:43 AM
|
|
Replies: 0
Views: 1,445
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, 06:48 AM
|
|
Replies: 0
Views: 1,780
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, 09:20 AM
|
|
Replies: 3
Views: 1,551
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, 06:54 AM
|
|
Replies: 3
Views: 1,551
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, 07:46 AM
|
|
Replies: 2
Views: 2,425
|
|
Forum: Bioinformatics
07-27-2009, 09:55 AM
|
|
Replies: 0
Views: 2,534
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, 09:25 AM
|
|
Replies: 2
Views: 2,425
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, 09:04 AM
|
|
Replies: 1
Views: 2,051
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, 10:23 AM
|
|
Replies: 0
Views: 2,426
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, 05:11 AM
|
|
Replies: 4
Views: 7,511
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, 03:11 AM
|
|
Replies: 0
Views: 1,631
HI
Hi all,
I am Paolo, italian postdoc working in South Africa.
Nice to hear about you!
|
