Question

Average insert size and standard deviation among R1 and R2 scRNA-seq 10X

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4.3 years ago

elb ▴ 250

Hi guys, I need to upload in a public repository single cell paired ends data from 10X, i.e. I have R1 and R2 .fastq files. While uploading the average insert size is required as well as the standard deviation among the R1 and R2 for each sample. I have no idea on how to calculate them. Data were demultiplexed and aligned using Cellranger v2.1. and chemistry v2. Can anyone give me some feedback. This is totally new to me.

Thank you in advance

RNA-Seq scRNA-Seq sequencing • 2.1k views

ADD COMMENT • link updated 4.3 years ago by GenoMax 141k • written 4.3 years ago by elb ▴ 250

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Which public repository is this? I have only seen GEO ask for insert size, but it is not required.

ADD REPLY • link 4.3 years ago by igor 13k

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Yes, GEO while preparing the metadata. They have a template and a section for "paired end experiments" that must be completed.

ADD REPLY • link 4.3 years ago by elb ▴ 250

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This is not really a paired-end experiment even though there are two read files.

ADD REPLY • link 4.3 years ago by GenoMax 141k

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Ooook so I think they will not ask me to add information about.

ADD REPLY • link 4.3 years ago by elb ▴ 250

score 1 · Answer 1 · 2019-12-28

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4.3 years ago

GenoMax 141k

Since only R2 is actual data used for alignments so you could calculate using the solutions here: Sequence Length Distribution From A Fastq File

R1 reads are UMI/cell barcodes, so they should all be same length.

ADD COMMENT • link 4.3 years ago by GenoMax 141k