FX on the Cloud

Run FX over the Amazon Web Service.
See FX AWS Web UI Document.

AWS Credentials

Sign up for Amazon Web Service, and subscribe for S3, Elastic MapReduce, Elastic Compute Cloud. For details, visit AWS at aws.amazon.com

AWS Access Key
AWS Secret Key

Define the Size of the Cloud

Instance Type
Details for instance types and pricing.
Number of Instances
If you wish to run more than 20 instances, complete the limit request form at AWS.

Project Directory

Point to the S3 URL for the project directory, the parent directory of "rawdata" or "align_results" directory. "rawdata" directory contains the raw FASTQ sequence files, and "align_results" contains the GSNAP result or SAM files.

Project URL

For example, if the s3 structure looks as following:
s3://fx-samples/sample_1/
align_cdna/
part-00000.result
part-00001.result
part-00003.sam
rawdata/
seq_14_pair1.fastq
seq_14_pair2.fastq
than put s3://fx-sample/sample_1 into the Project URL field.

Reference

hg19(Build 37) hg18(Build 36.3) mm9 Custom path
See how to make a custom reference

Configure Analysis Options

Run at Once
Step by Step

1. Preprocess I have a sam format file
This process splits raw FASTQ file for faster map-reduce manipulation and prepare for GSNAP alignment. Split into files
2. GSNAP Alignment options get result in sam format file
-m(max-mismatches) , -i(indel-penalty) ,
other options:
*You may leave it as it is
3. Base Call
From the alignment result, filter bases out under these criteria:
Filter bases under quality value of , quality encoding: Trim bases from each read ends to avoid adapter sequences
4. SNP Call
Count as SNP when allele appears more than x
Define as SNP when frequency over wildtype is greater than %
5. INDEL Call
Count as INDEL when allele appears more than x
Define as INDEL when frequency over wildtype is greater than %
6. Expression Profiling
Normalization Method : BPKM, FPKM
Similar to RPKM(FPKM), normalize profile expression level in base resolution of each gene (BPKM)
Filter as "expressed" with BPKM(FPKM) >
Gene Model : Union Gene Model, Union Intersection Model
Are you running Base Call? If NOT : Show
From the alignment result, filter bases out under these criteria:
Filter bases under quality value of , quality encoding: Trim bases from each read ends to avoid adapter sequences
7. Map Unmpped Reads against Reference Genome (optional)
-m(max-mismatches) , -i(indel-penalty) ,
Splice options:
other options:
*You may leave it as it is

Genomic Medicine Institute, Seoul National University College of Medicine, 28 Jongno-Gu, Yongon-Dong, Seoul 110-799, Korea