kathrinklee

Tool collection for epigenomic analysis

TopHat 2.1.1 with Bowtie 2.3.4.1

Using drop-seq-pipeline

RNA-seq pipeline including hisat2 v2.1.0, sratools v2.8.2 and stringtie v1.3.3b based on Ubuntu

STAR aligner 2.5.1b and samtools 0.1.19

MACS 2.1.0.20140616

MACS 1.4.2

Bowtie 2.2.4

Bowtie 1.1.1

Hisat 0.1.5-beta

Samtools 0.1.19

Picard 1.134

Tools (bowtie1, samtools-0.1.19-1, picard-tools-1.134, macs2) needed to process ATAC-Seq samples

Using drop-seq-tools 1.12 and STAR aligner 2.5.1

C1 analysis tools like STAR 2.5.1b and FastQC v0.11.5

Ubuntu with rna-seq analysis tools, sra-toolkit 2.4.4, kallisto and sleuth

HTSeq 0.6.1p1

BWA 0.7.12