###### 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.

---

## 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

---


---

## 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