Where Can I Find Already Mapped Reads ?

Question

[Radhouane Aniba]

Hi everyone,

i am in my way for developing an RNA-seq data analysis pipeline, and I have some theories to implement for further analysis which are planned to be implemented after aligning reads to a reference genome using Bowtie.

I want to test this part of the pipeline to an already aligned set of reads, no matter the original experiement, I want just some data to play with for that part of the pipeline.

As I am new to RNA-seq, I wanted to ask you when you go to GEO to download some RNA-seq data what are the files that should be downloaded.

I found SRA files in a single GEO entry, should i download them all and convert them to sSAM format ? What is then the best tool to convert SRA to SAM.

Thank you

Radhouane

Answer 1

[Rm]

Try these: GSE25840

ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/series/GSE25840/

http://genome.ucsc.edu/cgi-bin/hgFileUi?g=wgEncodeGisRnaSeq

Answer 2

[Drio]

One thousand genomes project