BCL to FASTQ

[tahamasoodi]

Hello Dears,

configureBclToFastq.pl --input-dir=/home/tahashafi/NGS/illumina/BaseCalls/ --output-dir=/FASTQ/home/tahashafi/Documents/ --sample-sheet=/Sheets/home/tahashafi/Documents/

Please anybody help me.

Regards

[Tom Bair]

Do you get an error. The only thing I see is that I usually point directly to a file with the --sample-sheet arg rather than just the directory, but what you have may work if you have a file named SampleSheet.csv in that directory

[aggp11]

I don't thin you need "=" signs in the command. Try replacing "=" with a blank space.

[tahamasoodi]

Error in bcl to fastq

Hi Tom Bair,

Thanks. It shows an error message that input dir does not exist.

[kmcarr]

tahamasoodi,

If I may first make a suggestion that you do not post the same question multiple times across these boards. Thus far you have started two threads and added to a dormant thread with this one question. Besides not being proper board etiquitte, having multiple threads ongoing makes it difficult for the community to know what answers may already have been given in one or another.

Putting together what you have said here and in other threads you say, 1) you have approximately 30 BCL files, 2) you do not have a sample sheet and 3) you do not have a config.xml file. Based on this I suspect that you are not using CASAVA properly and perhaps don't understand the relationship between BCL files and FASTQ read files. CASAVA needs much more than just BCL files as input, it is expected that CASAVA has the whole Illumina run directory to work with. It needs a sample sheet, it needs the config.xml file, it needs the position filres (.pos, .loc or .cloc depending on instrument type/software version). And 30 BCL files really doesn't represent a useful amount of data. One BCL represents the basecalls for one tile, of one lane for one cycle of sequencing. A 100 bp paired end run (with index) on the HiSeq would generate 80,256 BCL files.

Perhaps if you gave a little more background on how you ended up with a mere 30 BCL files and what you expect to use this data for then the community could better answer your question.