SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Default Change in CASAVA / BCL->FASTQ skruglyak Bioinformatics 20 11-19-2012 12:51 PM
BCL to FASTQ tahamasoodi Bioinformatics 4 07-29-2012 04:29 AM
Conversion from bcl format to fastq files kjaja Bioinformatics 5 09-14-2011 07:13 AM
CASAVA v1.8 (Bcl to Fastq) Kacper Illumina/Solexa 2 08-04-2011 09:08 PM
.bcl to *qseq.txt conversion E_Klee Illumina/Solexa 3 08-10-2010 01:19 PM

Reply
 
Thread Tools
Old 07-28-2012, 03:55 AM   #1
tahamasoodi
Success
 
Location: India

Join Date: May 2012
Posts: 130
Default BCL to FASTQ conversion error

I am using CASAVA 1.8.2 on a separate machine and trying to convert bcl files generated by Hiseq 2000 to fastq but I am getting an error message that config.xml file does not exist at /usr/local/lib/CASAVA-1.8.2/perl/Casava/Demultiplex.pm line 111.
Can anyone please help me out from this issue.
Thanks
tahamasoodi is offline   Reply With Quote
Old 07-28-2012, 08:35 PM   #2
seb567
Senior Member
 
Location: Québec, Canada

Join Date: Jul 2008
Posts: 260
Default

I think it may be trying to use a XML file as the sample sheet for demultiplexing your data.
Did you provide --sample-sheet ?

See https://github.com/sebhtml/FastDemul...with-CASAVA.sh
for an example.


Sébastien Boisvert


Quote:
Originally Posted by tahamasoodi View Post
I am using CASAVA 1.8.2 on a separate machine and trying to convert bcl files generated by Hiseq 2000 to fastq but I am getting an error message that config.xml file does not exist at /usr/local/lib/CASAVA-1.8.2/perl/Casava/Demultiplex.pm line 111.
Can anyone please help me out from this issue.
Thanks
seb567 is offline   Reply With Quote
Old 07-29-2012, 02:25 AM   #3
tahamasoodi
Success
 
Location: India

Join Date: May 2012
Posts: 130
Default Error in bcl to fastq

Thanks seb567, no I don't have a sample-sheet. I just want to convert bcl to fastq.
tahamasoodi is offline   Reply With Quote
Old 07-29-2012, 09:50 AM   #4
seb567
Senior Member
 
Location: Québec, Canada

Join Date: Jul 2008
Posts: 260
Default

In your run directory, you should have these files:


./Data/Intensities/BaseCalls/config.xml
./Data/Intensities/config.xml


I think they are missing in your case.
seb567 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 06:07 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO