To work on the intervals of the sequences - Operate on genomic intervals - Text Manipulation - Join, Subtract, and Group
Sequence quality control - FASTQ quality control - Fasta QC
To trim and manipulate data - FASTA/FASTQ
- Fasta Trimmer
- Fasta Quality trimmer
- Trim sequences
- FASTG Groomer
- Filter by quality
- Remove sequencing artifacts
Chip seq analysis - for alignment of reads - Bowtie2
- for peaks calling - MACS ( transcription factor binding )
- for histone modification - SICER
RNA-seq analysis - for alignment of reads - TopHat/ RNA STAR/ HiSat
- for assembly of transcripts - Cufflinks
- for merging transcript - Cuffmerge
- for measuring differential expression - Cuffdiff