Download RNASeq data

[Seb]

hi all

i'm confused about which RNA Seq data i should download for my analysis.

i am interested in seeing the RNA levels/reads in K562 cells (untreated). i know Caltech has all the different forms of it and here's where i'm a lil confused.

what i would need (if available) is the gene name with number of reads, or the chromosomal location with the number or reads. (kinda like a BED file)

which file should i go for?

do I need to further analyze the data?

thanks

[Steve Heitner]

Hello, Seb.

You can obtain the files you need by using the ENCODE file search tool.

1. Navigate to http://genome.ucsc.edu/cgi-bin/hgFileSearch?db=hg19

2. In the “Cell, tissue or DNA sample” line, click the text box and check the K562 checkbox

3. On the “Antibody or target protein” line, click the dropdown menu and change “Antibody or target protein” to “View – Peaks or Signals”

4. Click the text box next to “View – Peaks or Signals” and check the three “Exons Gencode” checkboxes

5. Click the “search” button

The resulting GTF files should contain the information you’re looking for.

Please contact us again at gen...@soe.ucsc.edu if you have any further questions.

---
Steve Heitner
UCSC Genome Bioinformatics Group

--
 
 
 

[Steve Heitner]

Hello again, Seb.

In step 4, you should select the “Genes Gencode” checkboxes instead of the “Exons Gencode” checkboxes.  I apologize for the confusion.

Please contact us again at gen...@soe.ucsc.edu if you have any further questions.

---
Steve Heitner
UCSC Genome Bioinformatics Group

[Seb]

hi Steve, 

thanks for the help, i found the file and i see that the reads are in this script

FPKM "0"

FPKM_lo "0"

FPKM_hi "0"

npIDR"0.953"

or 

FPKM "5.01575"

FPKM_lo "4.58019"

FPKM_hi "5.45131"

npIDR"0.009"

which one of those is the value that i have can use to represent the reads for that gene?

what does the npIDR value represent?

thanks so much !!

Seb

[Kate Rosenbloom]

Hi Seb,

The Gene-level file formats for the CSHL RNA-seq are described in the
Info text files in the Supplementary directory of the downloads for this
data:

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/supplemental/

As described there, the RPKM1-2 and FPKM1-2 values reflect enrichment
for each of two replicates.

Note that you can locate the downloads directory from File Search
results by clicking on the folder icon for your dataset of interest.

Additional information can be found in the track description for the
CSHL Long RNA-seq browser track, and you can email the lab contact
listed in the 'Credits' section for further details.

Cheers,
Kate
---
Kate Rosenbloom
UCSC Genome Bioinformatics

On 4/2/13 12:04 PM, Seb wrote:
> hi Steve,
>
> thanks for the help, i found the file and i see that the reads are in
> this script
>
> FPKM "0" FPKM_lo "0" FPKM_hi "0" npIDR"0.953"
>
>
> or
>
> FPKM "5.01575" FPKM_lo "4.58019" FPKM_hi "5.45131" npIDR"0.009"
>
>
> which one of those is the value that i have can use to represent the
> reads for that gene?
>
> what does the npIDR value represent?
>
> thanks so much !!
>
> Seb
>
>
> On Tue, Apr 2, 2013 at 12:23 PM, Steve Heitner <st...@soe.ucsc.edu
> <mailto:st...@soe.ucsc.edu>> wrote:
>
> Hello again, Seb.
>

> In step 4, you should select the �Genes Gencode� checkboxes
> instead of the �Exons Gencode� checkboxes. I apologize for the

> confusion.
>
>
>
> Please contact us again at gen...@soe.ucsc.edu

> <mailto:gen...@soe.ucsc.edu> if you have any further questions.

>
> ---
> Steve Heitner
> UCSC Genome Bioinformatics Group
>

> *From:*Steve Heitner [mailto:st...@soe.ucsc.edu
> <mailto:st...@soe.ucsc.edu>]
> *Sent:* Tuesday, April 02, 2013 8:33 AM
> *To:* 'Seb'; gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>
> *Cc:* ka...@soe.ucsc.edu <mailto:ka...@soe.ucsc.edu>
> *Subject:* RE: [genome] Download RNASeq data

>
> Hello, Seb.
>
> You can obtain the files you need by using the ENCODE file search
> tool.
>
> 1. Navigate to http://genome.ucsc.edu/cgi-bin/hgFileSearch?db=hg19
>

> 2. In the �Cell, tissue or DNA sample� line, click the text box

> and check the K562 checkbox
>

> 3. On the �Antibody or target protein� line, click the dropdown
> menu and change �Antibody or target protein� to �View � Peaks or
> Signals�
>
> 4. Click the text box next to �View � Peaks or Signals� and check
> the three �Exons Gencode� checkboxes
>
> 5. Click the �search� button
>
> The resulting GTF files should contain the information you�re

> looking for.
>
> Please contact us again at gen...@soe.ucsc.edu

> <mailto:gen...@soe.ucsc.edu> if you have any further questions.

>
> ---
> Steve Heitner
> UCSC Genome Bioinformatics Group
>

> *From:*gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>
> [mailto:gen...@soe.ucsc.edu] *On Behalf Of *Seb
> *Sent:* Monday, April 01, 2013 1:02 PM
> *To:* gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>
> *Subject:* [genome] Download RNASeq data