Project u12

Install

• You will need KorfLab/grimoire

Programs

• u12 - base program for doing stuff

Files

• 1pct.fa.gz - 1% of the A. thaliana genome
• 1pct.genes.gff3.gz - 1% of the A. thaliana genes
• 1pct.splice.gff3.gz - 1% of the A. thaliana splices (RNA-seq introns)
• at.genome.fa.gz - complete genome TAIR10
• at.genes.gff3.gz - complete set of genes TAIR10
• at.splices.gff3.gz - complete set of RNA-seq introns TAIR10
• at.introns.tsv.gz - the result of the Build procedure below

Build

Used the 1pct... files for testing.

./u12 introns --fasta 1pct.fa.gz --splices 1pct.splices.gff3.gz

This will output a tab-delimited file that looks something like below, which shows the chromosome, begin, end, strand, count, and sequence for every intron in the splices file.

Chr1    3877    3995    +       2       GTCAACATCTGTAG...
Chr1    3912    3993    -       2       GTTCAAAACAAAAA...
Chr1    3914    3995    +       1363    GTAAGTTCCGAATT...
Chr1    4277    4485    +       1021    GTTTTCTTCTATTC...

The introns for the entire genome result in an 87M file (16M compressed).

./u12 introns --fasta at.genome.fa.gz --splices at.splices.gff3.gz > at.introns.tsv
gzip introns.tsv

To find overlapping introns

./u12 overlap --introns at.introns.tsv.gz

Some stats about the splice sites

./u12 stats --introns at.introns.tsv.gz