Infer strandedness of my single-end RNA-Seq data
Entering edit mode
3.4 years ago
ATCG ▴ 380

Hi, I'm using to infer strandedness of my single-end RNA-Seq data

For Alignment using HISAT2 I used the genome

To use would I convert this genome.fa file to bed??

Or the GTF file corresponding to the .fa?

I tried using this bed file from the

but I get the following error: --input-file=WT_1.bam --refgene=dm6_Ensembl.bed --sample-size=200000 --mapq=30

Reading reference gene model dm6_Ensembl.bed ... Done Loading SAM/BAM file ... Finished Total 0 usable reads were sampled Unknown Data type

I have read other post on this topic but I still don't know how to solve this error

RNA-Seq HISAT2 strandedness • 964 views
Entering edit mode
3.4 years ago

I do not know about but since your question title is broad I'll mention an other approach. You can quantify known genes using a strand specific tool - then invert the strandness of the known annotation and do it again. By (for each gene) comparing how large a fraction read maps to the standard vs the inverted you can get an answer.


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