Hi @evolvedmicrobe and All,
I am interested to check the spectrum of lncRNA in 10X scRNA Seq data, towards which I have download few snRNA Seq possorted_genome_bam.bam from EGA and have generated their fastq files using 10x's bamtofastq. But when I align these fastqs with the ENSEMBL lncRNAs (reference generate by using cellranger's mkgtf) I am getting 0% alignment.
When I follow the same pipeline with scRNA Seq data it works well but have no clue why it is not working with snRNA Seq data.
PS: For some of my samples, bamtofastq has generated fastq files under the folder named with "MissingLibrary".
Has anybody tried this before? Can you please guide why I am not getting any alignment here?
Hi @evolvedmicrobe and All, I am interested to check the spectrum of lncRNA in 10X scRNA Seq data, towards which I have download few snRNA Seq possorted_genome_bam.bam from EGA and have generated their fastq files using 10x's bamtofastq. But when I align these fastqs with the ENSEMBL lncRNAs (reference generate by using cellranger's mkgtf) I am getting 0% alignment.
When I follow the same pipeline with scRNA Seq data it works well but have no clue why it is not working with snRNA Seq data.
PS: For some of my samples, bamtofastq has generated fastq files under the folder named with "MissingLibrary".
Has anybody tried this before? Can you please guide why I am not getting any alignment here?
Looking for your kind suggestions. Thanks