Process Illumina Sequencing Data.

Question

[María José]

Hi, I have recently received Illumina sequencing data from different cell lines, I wonder where I can access for documentation and resources to determine the best pipeline for processing these samples.

When I open FASTQ files, the ID of reads are as follow: LH00587:112:22LM2WLT4:1:1101:7199:1028. I understant that the instrument ID would be LH00587 and the flow cell ID is 22LM2WLT4. I would like to know how to identify the specific pipelines for the instrument and flow cell used

If anyone knows any resources or documentation for processing this type of data, I would greatly appreciate it!.

Answer 1

[GenoMax]

I would like to know how to identify the specific pipelines for the instrument and flow cell used

You normally do not need to worry about this part. Fastq data is equivalent (per Illumina guidance) no matter what flowcell/sequencer it may have been generated on. Quality scores may be binned (or not depending on sequencer) but generally they are not a big concern for data analysis.

Based on the flowcell ID "22LM2WLT4" this is likely data from a NextSeq 2000 P4 flowcell. See this prior post for more info --> Illumina Instrument Type from fastq?

where I can access for documentation and resources to determine the best pipeline for processing these samples.

Data analysis will depend on what kind of data this is (e.g. genome seq, RNAseq). Can you clarify what kind of data this is?