Parsing flowcell from hiseq 2000 read name
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5.4 years ago
steven.davis ▴ 10

Is there a way to extract instrument and flowcell from a read name like this:

>gnl|SRA|SRR1840614.1.1 FCC1KPRACXX:1:1101:1291:2172

FCC1KPRACXX : what is this?
1 = lane?
1101 = ?
1291 = x
2172 = y

I need to extract the flowcell if possible, so it can be assigned to reads downstream in a sam file read-group tag.

illumina fastq hiseq • 1.9k views
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Pierre's description of the numbers is correct. Additionally, I suspect it is theoretically possible to convert "FCC1KPRACXX" into an instrument, but I'm not aware of a tool that does that. That is a string that Illumina sticks on the beginning of sequence identifiers and certainly has meaning to them; so, I suggest you contact Illumina and ask them how to translate it into a specific instrument. If you get a useful response, I'd encourage you to post it here.

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5.4 years ago

https://en.wikipedia.org/wiki/FASTQ_format

FCC1KPRACXX : the flowcell id

1 = flowcell lane

1101 = tile number within the flowcell lane

1291 = 'x'-coordinate of the cluster within the tile

2172 = 'y'-coordinate of the cluster within the tile

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Thank you Pierre. I'm writing a Python module to parse the sequence ids and extract various data elements. I will put it on GitHub sometime soon.

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