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Abstract:
We describe an R package designed for processing aligned reads from chromatin-ori-
ented high-throughput sequencing experiments. Pasha (preprocessing of aligned sequences from
HTS analyses) allows easy manipulation of aligned reads from short-read sequencing technologies
(ChIP-seq, FAIRE-seq, MNase-Seq,
...
) and offers innovative approaches such as ChIP-seq reads
elongation, nucleosome midpoint piling strategy for positioning analyses, or the ability to subset
paired-end reads by groups of insert size that can contain biologically relevant information.
Availability and implementation:
Pasha is a multi-platform R package, available on CRAN reposito-
ries under GPL-3 license (https://cran.r-project.org/web/packages/Pasha/).
Contacts:
rfenouil@gmail.com or jean-christophe.andrau@igmm.cnrs.fr
Supplementary information:
Supplementary data
are available at
Bioinformatics
onlin
