Differences

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--- data:fastq [2025/08/19 15:27] – Moved quotes Richard Bowers
+++ data:fastq [2025/08/20 15:13] (current) – Removed mention of index quality for non-ATAC 10x Richard Bowers
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-====== FASTQ Files ======
+====== FASTQ Files and Index Reads ======
 Typically, our service will deliver one or two FASTQ files for your reads, one for each main part of the read sequence. We do not as a matter of course deliver FASTQ files for index reads. There are exceptions (discussed below), but for most cases there is no value in doing so and these files can significantly increase the size of your lane on disk for no benefit.
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 ===== "Unspecified Index" =====
-This is our "sequencing something novel at your own risk" option. For this we will not be sure what is in the index reads, if indeed they are indexes, so we will generate FASTQ for the index reads of this index type. // [[submission:indexkits#custom_indexing|See "Unspecified Index" on the Genomics Indexes page.]] //
+This is our "sequencing something novel at your own risk" option. For this we will not be sure what is in the index reads, if indeed they are indexes, so we will generate FASTQ for the index reads of this index type. // [[submission:indexkits#custom_indexing|See "Custom Indexing" on the Genomics Indexes page.]] //
-===== 10x Single Cell =====
+===== 10x Single Cell (excluding ATAC) =====
-//This excludes single cell ATAC and multiome ATAC. See below for both types of ATAC sequencing.//
+We do not generate FASTQ index reads for most single cell library types. We have had communication with 10x support and they have confirmed that not having the index read FASTQ makes no difference to the analysis. As such, the additional storage outweighs having a number for index read quality. The same logic as quoted earlier applies: would you re-demultiplex in a different way with index quality scores?
-We do not generate FASTQ index reads for most single cell library types. The **only** difference having these files available makes to the analysis is giving a number to the quality of the indexes in a CellRanger report. If these reads are not available CellRanger unfortunately reports this as a warning in the report, whereas (in our opinion) it should just quietly not report the value.
-We have had communication with 10x support and they have confirmed that not having the index read FASTQ makes no difference to the analysis. As such, the additional storage outweighs having a number for index read quality. The same logic as quoted earlier applies: would you re-demultiplex in a different way with index quality scores?
 ===== 10x ATAC =====