Zipped BCL to FastQ

[AmitChaurasia]

Hi Friends,

When I used CASAVA 1.8.2 to convert BCL to FastQ, it showd and error that *.bcl file not found. When I go to folder to check for the file i found *.bcl.gz file was present. In this way the conversion has failed.

Dear Friends, Is there any new command how to convert those zipped BCL file to FastQ format ?

Thanks.
Amit

[GenoMax]

Amit: It appears that you have data generated by a new version of HiSeq control software where the provider selected the option to zip the bcl files.

You will need to get bcl2fastq (v.1.8.3) software to handle the zipped files. You can download it here: http://support.illumina.com/download...tware_183.ilmn

Your data is likely to also have the Q-score binning applied as described in this white paper. http://support.illumina.com/download...footprint.ilmn.

[AmitChaurasia]

Dear GenoMax,

Thanks a lot for the reply, YEs our HiSeq got upgraded to 2500 from 2000 and hence the option of Zipped BCL file have been selected.

I have followed you instructions and the job has been completed succefully

Gr8 !

Thanks again.

Best
Amit Chaurasia

[PabloMarin-Garcia]

Just an update: the new version of BCL2FASTQ is out (v1.8.4):

http://support.illumina.com/downloads/bcl2fastq_conversion_software_184.ilmn

It has improved the adaptor cleaning and the trimming is different.