Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
BFAST - Help cutcopy11 SOLiD 17 10-17-2013 07:12 AM
BFAST indexing phatjoe Bioinformatics 1 09-08-2011 07:39 PM
BFAST using GPUs nikhil.stephen Bioinformatics 7 02-20-2011 10:14 PM
BFAST thanks you for your help! (was: ... needs your help) nilshomer Bioinformatics 5 04-21-2010 07:29 PM
Bfast jsun529 Bioinformatics 19 11-12-2009 08:32 AM

Thread Tools
Old 07-12-2010, 03:37 AM   #1
Senior Member
Location: Germany

Join Date: May 2010
Posts: 101
Default BFAST configuration

Could anyone please provide a working config file for to use as an example? We tried to create a config file, but it's sometimes hard to guess which parameter name in the schema stands for which in the BFAST programs. Also, Eclipse reports that the provided xml schema is incorrect at some places. Despite our efforts, the exited without producing output. (We're using the data from the latest BFAST version.) looks like a valuable tool and it would be very useful to get it to run for our cluster.

In that context, I'd like to know what the most efficient way of running BFAST is. I can use a node with 16 CPUs, up to 128 GB RAM. The 10 indexes for the human genome are 12 GB each so it's probably impossible to load them all into memory and keep enough space for the rest, especially when using pipes. As I noted, reading the indexes (one at a time as done by default) is the most time-consuming part in our case. Instead of splitting up the reads much and call multiple instances of bfast match with all indexes, I think it would be better to process all reads with one of the indexes in parallel.

Thanks in advance for the help

epigen is offline   Reply With Quote
Old 03-18-2011, 06:51 AM   #2
Junior Member
Location: Barcellona

Join Date: Feb 2011
Posts: 4

this is my config file.
I have not a sam file in the output, but only some sh script:,,,
I don't know what is the next step because, as i write you, it's sometimes hard to guess which parameter name in the schema stands for which in the BFAST programs.
A suggestion:
if you have any validation errors with eclipse don't worry, they're not preclude the running of bfast.
I am a beginner so i don't know if this can help you. I hope..
Anyway, this is the BASIC xml version to run it:
<?xml version="1.0" encoding="UTF-8"?>
<bfastConfig xmlns:xsi="" xsi:noNamespaceSchemaLocation="BfastConfig_5.xsd">
<numReadsPerFASTQ localalignSplit="20" matchSplit="20">20</numReadsPerFASTQ>

To add any parameter, you can inspire from XSD and from
If you solved it, please share your code.
Thanks a lot.
Vincenzo is offline   Reply With Quote

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 04:27 PM.

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