Built an rna-seq pipeline for paired end reads.
Got single end data and had to revise.
Only problem I have now is the rseqc infer_Experiment strand_rule.
I am trying to run bam2big.py and it's not recognizing the strand_rule I'm inputting.
What are the strand rule options for single end reads?
Aren't they just, ++,-- or +-,-+?
Anyone encounter a problem like this before? Or is it always none because it's a single end read?
Got single end data and had to revise.
Only problem I have now is the rseqc infer_Experiment strand_rule.
I am trying to run bam2big.py and it's not recognizing the strand_rule I'm inputting.
What are the strand rule options for single end reads?
Aren't they just, ++,-- or +-,-+?
Anyone encounter a problem like this before? Or is it always none because it's a single end read?