European Molecular Biology Laboratory - Haley Sharpe Design



HTSeq – a Python framework
* facilitates rapid development of NGS data analysis scripts
* initial release in 2010, latest update published 2022
* allows users with moderate Python knowledge to create scripts, shields more advanced internals
from the user
*
* HTSeq-count – a tool for preprocessing RNA-Seq data for differential expression analysis

•SAM/BAM
GTF/GFF
•
•how many aligned reads overlap exon/union of exons
•designed for differential expression analysis
•default setting counts unambiguously mapped reads only
•discards reads mapping to multiple positions or overlapping multiple features
•for pair-end counts fragments, not reads
•
•table with
•counts for each feature
special counters (reads that were not counted for any feature)
HTSeq-count

Looks like BAM and GFF file types are still an option.
   https://htseq.readthedocs.io/en/master/features.html?highlight=gff#HTSeq.GFF_Reader
   https://htseq.readthedocs.io/en/master/tutorials/bam_reader.html?highlight=bam

•If a read maps on multiple features:
•
•--nonunique none (default)
•--nonunique all
•--nonunique fraction
•--nonunique random
•