Genomics: analysis and algorithms - Exercise 5

Analysis of real ht-data

You have pooled data from the sequencing service. This is a special version of RNA-Seq, the RNA was fragmented to 200 bp, single end, ion-torrent. A total of 4 libraries, marked with a barcode on both sides. From the ex3.fastq file:

• check the quality of the sequencing run: fastqc (reference)
• split fastq into four files by library
• calculate the statistics of the representation of individual libraries
• remove all adapters and keep only sequences longer than 25 bp: fastx, cutadapt, trimmomatic, (your own?)
• count statistics (number of sequences and total number of bases before and after removing adapters)

barcodes

	ex3-smpl1.f       MID1    ACGAGTGCGTACACGACGCTCTTCCGATCT
	ex3-smpl1.r       MID3    AGACGCACTCCAGACGTGTGCTCTTCCGATCT
	ex3-ctrl1.f       MID5    ATCAGACACGACACGACGCTCTTCCGATCT
	ex3-ctrl1.r       MID7    CGTGTCTCTACAGACGTGTGCTCTTCCGATCT
	ex3-smpl2.f       MID11   TGATACGTCTACACGACGCTCTTCCGATCT
	ex3-smpl2.r       MID14   CGAGAGATACCAGACGTGTGCTCTTCCGATCT
	ex3-ctrl1.f       MID12   TACTGAGCTAACACGACGCTCTTCCGATCT
	ex3-ctrl2.r       MID18   TCTACGTAGCCAGACGTGTGCTCTTCCGATCT