SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
RNA-Seq: Genome Wide Full-Length Transcript Analysis Using 5' and 3' Paired-End-Tag N Newsbot! Literature Watch 1 01-20-2012 06:38 PM
RNA-Seq: Full-length transcriptome assembly from RNA-Seq data without a reference gen Newsbot! Literature Watch 7 10-26-2011 06:37 AM
Roche gsMapper output exon contigs rather than full-length sequence? sulicon Bioinformatics 0 02-28-2011 05:51 PM
TopHat & Cufflinks failing to assemble full length transcripts jlhaner Bioinformatics 3 10-13-2010 11:46 AM
PubMed: Use of massive parallel pyrosequencing for near full-length characterization Newsbot! Literature Watch 0 09-16-2009 03:00 AM

Reply
 
Thread Tools
Old 05-18-2010, 12:00 AM   #1
zslee
Member
 
Location: shanghai of china

Join Date: May 2009
Posts: 29
Default about UCSC full length cDNA

in one paper, they use downloaded full length cDNA sequences(from ucsc) to detect A-to-I rna editing by aligning to reference hg16, but when i want to repeat their work by downloading human mRNA sequences(i think this is the data they used), i find there's no difference between the mRNA sequences and hg16, why? did i use the wrong data?

can anyone give me a hint
thanks in advance
zslee is offline   Reply With Quote
Old 05-18-2010, 03:10 AM   #2
jiaco
Member
 
Location: GMT +1

Join Date: May 2010
Posts: 35
Default

Is this really the first post in a thread or is my browser messed up? I hope that my reply here can actually be considered constructive, as intended.

Quote:
Originally Posted by zslee View Post
in one paper,
what paper?

Quote:
Originally Posted by zslee View Post
by downloading human mRNA sequences
from where? which file(s)

Quote:
Originally Posted by zslee View Post
(i think this is the data they used)
This appears to be the crux of your problem, you do not know what data they used and therefore cannot download it, and cannot repeat their work.

But again, what paper?

Quote:
Originally Posted by zslee View Post
why? did i use the wrong data?
I honestly have no idea based on the info in your post.
jiaco is offline   Reply With Quote
Old 05-18-2010, 03:29 AM   #3
zslee
Member
 
Location: shanghai of china

Join Date: May 2009
Posts: 29
Default yes, i should make it clear ~

the paper i consider is
"Widespread RNA editing of embedded alu elements in the human transcriptome"
in the method part, they mentioned "We obtained all human and mouse full-length cDNA sequences from the UCSC Genome Browser database and aligned them against their reference genome sequences using BLAT"

my problem is i don't know where to download the full length cDNA sequences from UCSC database

thanks
zslee is offline   Reply With Quote
Old 05-18-2010, 03:44 AM   #4
jiaco
Member
 
Location: GMT +1

Join Date: May 2010
Posts: 35
Default

From http://genome.ucsc.edu/
click Tables
then select the following form entries

Mammal : Human : Mar2006 (or the assembly you want)
Genes and Gene Prediction Tracks : UCSC Genes
knownGene
region: genome

outputformat: sequence
set an output file name
use gzip compression

get output

on the next page, you can select mRNA which will splice out introns and start the download of all ucsc known gene mRNA sequences in fasta format.

(but this is really a question for UCSC genome browser, no?)
jiaco is offline   Reply With Quote
Old 05-18-2010, 03:52 AM   #5
steven
Senior Member
 
Location: Southern France

Join Date: Aug 2009
Posts: 269
Default

Quote:
Originally Posted by zslee View Post
in one paper, they use downloaded full length cDNA sequences(from ucsc) to detect A-to-I rna editing by aligning to reference hg16, but when i want to repeat their work by downloading human mRNA sequences(i think this is the data they used), i find there's no difference between the mRNA sequences and hg16, why? did i use the wrong data?

can anyone give me a hint
thanks in advance
Yep indeed, looks like if you go to "Tables" then select group=mRNAs and ESTs, track=human mRNAs, then table=all_mrna, the output=sequence sends you to "Human mRNAs *Genomic* Sequence", which i understand is a genomic extraction based on the positions from the alignments, which is obviously not what you want.
To get the original transcript sequences, try with table=RefSeq Genes instead, you will be given the choice between genomic, protein and mRNA.
I bet the later works for you.
cheers,
s.
steven is offline   Reply With Quote
Old 05-18-2010, 04:08 AM   #6
zslee
Member
 
Location: shanghai of china

Join Date: May 2009
Posts: 29
Red face

Quote:
Originally Posted by jiaco View Post
From http://genome.ucsc.edu/
click Tables
then select the following form entries

Mammal : Human : Mar2006 (or the assembly you want)
Genes and Gene Prediction Tracks : UCSC Genes
knownGene
region: genome

outputformat: sequence
set an output file name
use gzip compression

get output

on the next page, you can select mRNA which will splice out introns and start the download of all ucsc known gene mRNA sequences in fasta format.

(but this is really a question for UCSC genome browser, no?)
yes, i've tried, it works, thanks to jiaco !
and i'm not familiar with UCSC
zslee is offline   Reply With Quote
Old 05-18-2010, 04:11 AM   #7
zslee
Member
 
Location: shanghai of china

Join Date: May 2009
Posts: 29
Default

Quote:
Originally Posted by steven View Post
Yep indeed, looks like if you go to "Tables" then select group=mRNAs and ESTs, track=human mRNAs, then table=all_mrna, the output=sequence sends you to "Human mRNAs *Genomic* Sequence", which i understand is a genomic extraction based on the positions from the alignments, which is obviously not what you want.
To get the original transcript sequences, try with table=RefSeq Genes instead, you will be given the choice between genomic, protein and mRNA.
I bet the later works for you.
cheers,
s.
yes, just as you mentioned, i need mRNA not genomic sequences,
and in the paper i considered, they download data same as jiaco's suggestion
thanks to steven !
zslee is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 08:24 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO