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Forum: Illumina/Solexa 12-22-2008, 04:47 AM
Replies: 0
Views: 1,954
Posted By fabio25
solexa protocol: unique tags

Dear everybody,
I'm trring to understand how solexa sequencing works. Probably what I'm doing it's really a very stupid question, but I'm not able to understand it.
The basic protocol for chip-seq...
Forum: Bioinformatics 12-17-2008, 02:51 AM
Replies: 20
Views: 11,118
Posted By fabio25
Solid VS Solexa

Dear Everybody,
I would like to ask if someone can help me to understand the difference among the Solid machine and the Solexa one. Which tools are used to analyze such type of data and which is the...
Forum: Bioinformatics 11-12-2008, 09:04 AM
Replies: 52
Views: 82,346
Posted By fabio25
Dear everybody, I would be very interested in...

Dear everybody,
I would be very interested in asking how you fix the miRNA targets.
just use mirBASE or have you a much nicer way?
Thanks a lot,
Fabio
Forum: Bioinformatics 09-25-2008, 03:16 AM
Replies: 3
Views: 2,105
Posted By fabio25
hi Eco, thank you a lot for the annoj advice. I'm...

hi Eco, thank you a lot for the annoj advice. I'm contacting the AnnoJ persone to ask the same question and I'll see what he tells me. According to you, is it possible to get a new genome, in which...
Forum: Bioinformatics 09-24-2008, 04:20 AM
Replies: 3
Views: 2,105
Posted By fabio25
Exclamation from CGH arrays to genome map

Dear everybody
it's still me...with a strange question! I'm analyzing data from leukemia cell lines, presenting different translocations. I saw publicly available the CGH arrays from these cell...
Forum: Bioinformatics 08-27-2008, 02:02 AM
Replies: 19
Views: 4,067
Posted By fabio25
by fabio

hi zee
thanks for your answer. I was thinking like you at the beginning and so I took the track in the USCS browser and I brought it galaxy. If you do that with a bed file already present in the...
Forum: Bioinformatics 08-26-2008, 05:14 PM
Replies: 19
Views: 4,067
Posted By fabio25
hi kmay, I would like to do that, but the data...

hi kmay,
I would like to do that, but the data are not mine and I cannot send them.
However, I'm ostinate to find an open source way how to deal with these data, but if I'm not able I'll work...
Forum: Bioinformatics 08-26-2008, 05:03 PM
Replies: 19
Views: 4,067
Posted By fabio25
hi dcfargo i did that, but it's not so...

hi dcfargo
i did that, but it's not so precised. I retrieves me even te genes around doing it in R. probably I 'll have to try on the website.
Forum: Bioinformatics 08-26-2008, 09:52 AM
Replies: 19
Views: 4,067
Posted By fabio25
by fabio

hi Gbucci
thanks a lot for your advise. I tried one time to work with it but it dxoesn't work so fine with custom track in wiz format. probably it's me and I'll try again. May I ask you what do you...
Forum: Bioinformatics 08-03-2008, 09:14 AM
Replies: 19
Views: 4,067
Posted By fabio25
hi Kmay, thank you very much for your help. I...

hi Kmay,
thank you very much for your help. I was trying to use the RegionMiner (genomatix), but my bed file (raw data)was to0 big, aroung 60 Mb and the server told me that I cannot up-load it. Then...
Forum: Bioinformatics 08-03-2008, 08:35 AM
Replies: 19
Views: 4,067
Posted By fabio25
hi eco thank you very much for your reply. My...

hi eco thank you very much for your reply. My problem is that I'm not familiar with Perl scripting, and so I'll start to learn it. Untill now I worked only in R and bioconductor, but unfortunately I...
Forum: Bioinformatics 08-03-2008, 07:20 AM
Replies: 19
Views: 4,067
Posted By fabio25
Question retrieve gene name

Hi everybody,
I'm fabio and I wished to ask you if anybody knows how to retrieve from the genomic locations the gene name. Up to now I'm using the USCS genome browser, but It's quite complex to...
Forum: Introductions 08-03-2008, 07:07 AM
Replies: 0
Views: 44,173
Posted By fabio25
Smile hi, I'm Fabio.

Dear everybody,
I'm Fabio, an italian phD student. Untill now I worked only with transcryptomic data and just now I started to work with chip-seq data. I'm glad to make part of this great community....
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