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# System prepended metadata

title: 【ILMN】 ILMN BaseSpace Upload fastq files rules
tags: [upload, fastq, illumina, basespace]

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###### tags: `upload` `fastq` `basespace` `illumina`
# 【ILMN】 ILMN BaseSpace Upload fastq files rules

> [name= Bioinformatician Jeffrey C.H. Yu]

- Issue:
Upload FastQ files to BaseSpace, but fail cause by passing filter fail.

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## Illumina FASTQ file standard

- The uploader will only support gzipped FASTQ files generated on Illumina instruments.
- **The name of the FASTQ files** must conform to the following convention:   

__SampleName\_SampleNumber\_Lane\_Read\_FlowCellIndex.fastq.gz__
e.g.,
SampleName\_S1\_L001\_R1\_001.fastq.gz / SampleName\_S1\_L001\_R2\_001.fastq.gz


- **The read descriptor in the FASTQ files** must conform to the following convention:   
**@Instrument:RunID:FlowCellID:Lane:Tile:X:Y\[:UMI\] ReadNum:FilterFlag:0:SampleNumber**
where **\[:UMI\]** is an optional additional field
  - Read 1 descriptor would look like this:   
        @M00900:62:000000000-A2CYG:1:1101:18016:2491 1:N:0:13
  - Read 2 would have a 2 in the ReadNum field, like this:   
        @M00900:62:000000000-A2CYG:1:1101:18016:2491 2:N:0:13
  - Read 1 descriptor including UMI would look like this:   
        @M00900:62:000000000-A2CYG:1:1101:18016:2491:GCTAGCCTAG 1:N:0:13
  - Read 2 descriptor including UMI would look like this:   
        @M00900:62:000000000-A2CYG:1:1101:18016:2491:GCTAGCCTAG 2:N:0:13

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![](https://i.imgur.com/zfEgF0M.png)


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## Quality considerations
-   The number of base calls for each read must equal the number of quality scores
-   The number of entries for Read 1 must equal the number of entries for Read 2
-   The uploader will determine if files are paired-end based on the matching file names in which the only difference is the ReadNum
-   For paired-end reads, the descriptor must match for every entry for both reads 1 and 2
-   Each read has passed filter


![](https://i.imgur.com/FM5dsKo.png)
