FASTA to Seurat Object

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2.1 years ago

AbsaR • 0

I want to create seurat object from fasta files. I have illumina sequences, 2 .fasta files for each samples..... any pipeline to follow ?

data fasta seurat preprocessing • 1.2k views

ADD COMMENT • link 2.1 years ago by AbsaR • 0

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I assume you mean fastq files? See Cell Ranger, alevin-fry, or STARsolo documentation.

ADD REPLY • link 2.1 years ago by rpolicastro 13k

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i am using starsolo on galaxy but i am getting the following error

EXITING because of FATAL ERROR in input read file: the total length of barcode sequence is 100 not equal to expected 28 Read ID=>SRR2431431.1 ; Sequence=ACTTAAAGGAATGTGGGCTTTATTGAGAGGATGGCATAGTAAAAGCTATTACAGGGAGGAGTGTTGAGACCAGATGTCATCTACTGTCTCTTGGGTCAGC SOLUTION: check the formatting of input read files. If UMI+CB length is not equal to the barcode read length, specify barcode read length with --soloBarcodeReadLength To avoid checking of barcode read length, specify --soloBarcodeReadLength 0

Does it mean that the RNA seq data is not 10x Chromium ? How to solve this error ?

ADD REPLY • link 2.1 years ago by AbsaR • 0

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for reference i am using E-GEOD-73121 dataset, and working with single cell rna seq of patients metastatic samples only

ADD REPLY • link 2.1 years ago by AbsaR • 0

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