I have a question regarding the reads that are used in the collapsing step.
If I use the "generate_map" option, the number of reads that I get from the _combined.isoform.read.map.txt should be the same as the number of reads that are in the _all.corrected.bed that is the output of flair correct?
Surprisingly, sometimes I get more reads in the _combined.isoform.read.map.txt file than in the _all.corrected.bed file.
I have a question regarding the reads that are used in the collapsing step. If I use the "generate_map" option, the number of reads that I get from the _combined.isoform.read.map.txt should be the same as the number of reads that are in the _all.corrected.bed that is the output of flair correct?
Surprisingly, sometimes I get more reads in the _combined.isoform.read.map.txt file than in the _all.corrected.bed file.