BEDOPS [11] | BEDTools [10] | featureCounts [25] | CAP-miRSeq [8] | HOMER [9] | RSeqQC [26] | bam2x [12] | CEAS [7] | ALFA | |
---|---|---|---|---|---|---|---|---|---|
One line call | ✔⃞ | ✔⃞ | ✔⃞ | ✔⃞ | ✔⃞ | ✔⃞ | |||
Multiple samples | ✔⃞ | ✔⃞ | ✔⃞ | ||||||
Nucleotide resolution | ✔⃞ | ✔⃞ | ✔⃞ | ||||||
Hierarchical priorities | ✔⃞ | ✔⃞ | ✔⃞ | ✔⃞ | ✔⃞ | ✔⃞ | |||
Enrichment score | ✔⃞ | ✔⃞ | ✔⃞ | ||||||
Categories | ✔⃞ | ✔⃞ | ✔⃞ | ✔⃞ | ✔⃞ | ✔⃞ | ✔⃞ | ✔⃞ | |
Biotypes | ✔⃞ | ✔⃞ | ✔⃞ | ✔⃞ | ✔⃞ | ||||
Graphical output | ✔⃞ | ✔⃞ | ✔⃞ | ✔⃞ | |||||
Any NGS data | ✔⃞ | ✔⃞ | ✔⃞ | ✔⃞ | ✔⃞ | ✔⃞ |