Chromium Controller

• What is the purpose of loading surrogate fluid in the unused wells of the Chromium Chip?
• How do I decontaminate my Chromium Controller?
• What are the specs of the Chromium instrument?
• How do I clean my Chromium Controller instrument?
• Is the performance of the Chromium affected at high temperatures or humidity?
• Can the Chromium Controller be moved between labs?

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Reagents

• Why is it critical to load the wells in the specified order?
• What is the maximum number of thaw-freeze cycles for the i7 sample index plate?
• Can I mix reagents from different kits?
• What is the shelf life of 10x reagents?
• Can I pool leftover gel beads?
• Will failure in one channel affect samples in other channels?

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GEM Generation & Barcoding

• Which thermal cyclers are supported for use with GEMs?

Library Construction

• Why do I need to use qPCR to quantify my final library?
• How are SPRIselect volumes calculated?

Sequencing

• Why are there unequal ratios of the four oligos (or oligo dropout) in my 10x library after sequencing
• What oligos are in my sample index?
• Is a sample sheet required for sequencing?
• Is the i7 Sample Index plate compatible across products?
• Is the Sample Index PCR required if not multiplexing samples?

Software

• How to convert 10x BAM files to FASTQ files while preserving the barcode information?
• Should I trim the reads in my FASTQ files?
• How do I identify the unmapped reads in my Cell Ranger or Long Ranger output?
• How do I demultiplex my data if I only sequenced 7 bp on the index read?
• What bcl2fastq parameters does mkfastq use internally?
• How do I get help with a failed mkfastq run?

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