Hi, I'm using infer_experiment.py to infer strandedness of my single-end RNA-Seq data
For Alignment using HISAT2 I used the genome ftp://ftp.ensembl.org/pub/release99/fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP6.28.dna.toplevel.fa.gz
To use infer_experiment.py 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:
infer_experiment.py --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