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Old 12-13-2011, 04:56 PM   #81
sparks
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Hi Gabriele,
I never found out about the control bits. The is_filtered is a flag that Illumina sets if they think the read might be from a polyclonal cluster.
Colin
Quote:
Originally Posted by olus View Post
Hi Colin.
Did find out what
<control number>
in '@' FASTQ line is used for?

Except the light definition in the official pdf I couldn't find any suggestion.

If anybody could give me some hints it would be really appreciated!

Gabriele
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Old 12-14-2011, 07:59 AM   #82
olus
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Originally Posted by sparks View Post
Hi Gabriele,
I never found out about the control bits. The is_filtered is a flag that Illumina sets if they think the read might be from a polyclonal cluster.
Colin
Thank you for your reply.
At the end I found some clues of what it could be.
It seems that the bit value is inherited from the .control files and store the information about the eventual PhiX spike in, barcode mismatches etc...:

Cheers

Gabriele



(look at OLB_UG_15009920C.pdf from illumina)
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Old 05-14-2012, 03:41 AM   #83
boetsie
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Hi all,

For our Illumina HiSeq2000 we use the phiX spike-in. However, we see after demultiplexing that around 0.05% of the produced reads can align to the phiX genome. We now have a script that filters out the reads/pairs out that can align to the phiX genome (with Bowtie). This works ok, but we are wondering if there is an automated way to do this within CASAVA or if there is some flag within the fastQ header that represents if a read comes from the phiX genome?

Regards,
Boetsie
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Old 07-29-2012, 03:03 AM   #84
tahamasoodi
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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
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Old 07-29-2012, 09:47 AM   #85
sklages
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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
Hmm, it tells you that there is no config.xml file found within the run directory you have supplied. What is the command line you used for bcl conversion? Do you have access to the whole run and all of its files?

Sven
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Old 07-29-2012, 10:12 AM   #86
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Hi Sklages,
Thanks a lot. I have used the following command
configureBclToFastq.pl --input-dir /home/tahashafi/NGS/illumina/Base_Calls/C1.1 --output-dir /home/tahashafi/Desktop/casava_example_dir --Sample-Sheet /home/tahashafi/NGS/illumina/Base_Calls/C1.1/SampleSheet.csv --mismatch=1 --force --use-bases-mask Y101,I7,Y101

No I don't have access to the whole run and its files. Actually I have copied only some bcl files from the instrument connected machine and now am trying to convert those files to fastq on a separate machine.
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Old 07-29-2012, 10:14 AM   #87
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Hi Sklages,
Thanks a lot. I have used the following command
configureBclToFastq.pl --input-dir /home/tahashafi/NGS/illumina/Base_Calls/C1.1 --output-dir /home/tahashafi/Desktop/casava_example_dir --Sample-Sheet /home/tahashafi/NGS/illumina/Base_Calls/C1.1/SampleSheet.csv --mismatch=1 --force --use-bases-mask Y101,I7,Y101

No I don't have access to the whole run and its files. Actually I have copied only some bcl files from the instrument connected machine and now am trying to convert those files to fastq on a separate machine.
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Old 07-29-2012, 10:41 AM   #88
sklages
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Quote:
Originally Posted by tahamasoodi View Post
Hi Sklages,
Thanks a lot. I have used the following command
configureBclToFastq.pl --input-dir /home/tahashafi/NGS/illumina/Base_Calls/C1.1 --output-dir /home/tahashafi/Desktop/casava_example_dir --Sample-Sheet /home/tahashafi/NGS/illumina/Base_Calls/C1.1/SampleSheet.csv --mismatch=1 --force --use-bases-mask Y101,I7,Y101

No I don't have access to the whole run and its files. Actually I have copied only some bcl files from the instrument connected machine and now am trying to convert those files to fastq on a separate machine.
Well that's not enough. The software needs more than just the BCL files; e.g. it also needs config.xml (among others). You usually convert the whole flowcell from BCL to fastq as most people want to have fastq files at the end. So if you generated the data by yourself just copy the whole run and do the conversion or run the conversion on the machine where the complete data resides. If you have gotten the data from a sequencing provider just ask them to do the converision for you (including demultiplexing).


hth, Sven
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Old 07-30-2012, 10:02 PM   #89
tahamasoodi
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Quote:
Originally Posted by sklages View Post
Well that's not enough. The software needs more than just the BCL files; e.g. it also needs config.xml (among others). You usually convert the whole flowcell from BCL to fastq as most people want to have fastq files at the end. So if you generated the data by yourself just copy the whole run and do the conversion or run the conversion on the machine where the complete data resides. If you have gotten the data from a sequencing provider just ask them to do the converision for you (including demultiplexing).


hth, Sven

Thanks. Can I run it on a separate machine while connecting that machine via LAN to the the instrument machine where I have the whole flowcell data as it takes long time copying from the one machine to another?
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Old 07-30-2012, 10:18 PM   #90
sklages
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Quote:
Originally Posted by tahamasoodi View Post
Thanks. Can I run it on a separate machine while connecting that machine via LAN to the the instrument machine where I have the whole flowcell data as it takes long time copying from the one machine to another?
Yes, that's possible. At least with NFS. Keep in mind that this work slower as for local storage as the whole data needs to be read.

Let us know if it worked for you.

Sven
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