How to Analyze 10x Genomics Data with Full-Length R1 and R2 (100bp Each)?
Dear Biostars community,
I’m used to analyzing 10x Genomics single-cell RNA-seq data where R1 is typically 26bp (cell barcode + UMI) and R2 is longer (~100bp, cDNA read). However, I’ve encountered a dataset (GSM6782325) where both R1 and R2 are 100bp long, which is unusual (at least for me) for standard 10x data.
From what I understand, the R1 contains full sequencing of the polyA. I’m however, unsure how to analyze this type of sequencing data properly. Is this still valid 10x data? Does Cell Ranger support processing this, or do I need custom preprocessing?
Thanks in advance!
1 answer
Log in to answer this question.
More posts like this
-
SRA Toolkit - three fastq files - which is which?
written by Neat •
-
cell ranger low correct barcodes and failed
written by shersky •
-
how to convert using sratoolkit or fast-dump
written by shersky •
-
4 Fastq files for a single run generated by 10X
written by hkarakurt
-
Extract the true single-cell RNA sequencing reads for running SAHMI
written by 573704669 •
-
UMI in seqc2 dataset Burning Rock data
written by PeterWu •
-
Downloading smart-seq2 fastq files from NCBI GEO
written by malonzm1 •
-
Help needed with sra-toolkit; Does not show 3 files as per intended
written by SeroroO •
-
10x 3' library creates R1 and R2 fastq files with the same read length
written by tomas4482 •
-
Tutorial: scRNA-seq CITE-seq-count bioinformatics
written by colindaven
