sj2psi 0.1.2

Convert RNA-STAR SJ.out.tab files to 5-prime and 3-prime "percent spliced in" ("psi") scores.

[[](https://travis-ci.org/olgabot/sj2psi)](https://travis-ci.org/olgabot/sj2psi)[](https://coveralls.io/r/olgabot/sj2psi?branch=master)

DOI: 10.5281/zenodo.9885

Annotation-free estimation of percent spliced in of a junction. This will convert [RNA-STAR aligner](http://bioinformatics.oxfordjournals.org/content/29/1/15.long) “SJ.out.tab” files to “Percent spliced-in” (Psi) scores. Here’s an example of an SJ.out.tab file:

` chr1 30040 30563 1 1 1 0 131 45 chr1 30668 30975 1 1 1 0 123 46 chr1 146510 155766 2 2 1 50 92 46 chr1 155832 694346 2 2 0 6 14 26 chr1 317782 322037 1 1 1 0 2 3 chr1 320939 321031 1 1 1 2 4 31 chr1 322229 324287 1 1 1 0 3 21 chr1 322229 324438 1 1 0 0 5 40 chr1 324346 324438 1 1 1 0 2 13 chr1 324711 325802 2 4 0 0 1 30 chr1 663813 664904 2 4 0 0 1 38 chr1 665185 667396 2 2 0 0 2 37 chr1 665185 670802 2 2 0 0 4 40 chr1 667588 682074 2 2 0 0 44 43 chr1 668594 670802 2 2 0 0 4 40 chr1 670994 682074 2 2 0 0 47 43 `

As described in [Pervouchine et al, Bioinformatics (2013)](http://bioinformatics.oxfordjournals.org/content/29/2/273.long), we will take the approach of asking, how often is this donor site (5’ splice site) used with this acceptor site (3’ splice site), compared to ALL OTHER acceptors?

Same goes for acceptor sites. How often is this acceptor site, used with this donor site, compared to ALL OTHER donors?

To illustrate, check out this example. Each “-” represents 10 bp

Splice junction fig genome location number of reads [ ]——–[ ] chr1:100-180 90 [ ]———-[ ] chr1:100-200 10 [ ]——-[ ] chr1:130-200 40

For the 5’ splice site chr1:100, we have 90+10 = 100 total reads. Thus the “psi5” for chr1:100-180 is 90/100 = 0.9, and 0.1 for chr:100-200.

For the 3’ splice site chr1:200, we have 10+40 = 50 total reads. Thus the “psi3” for chr1:100-200 is 10/50 = 0.2, and 0.8 for chr:130-200.

What’s left is the uninteresting splice sites of chr1:180 and chr1:130, both of which didn’t have any variance and were always used. Thus psi3 for chr1:180 is 1.0, and psi5 for chr1:130 is 1.0 as well.

>>> import pandas as pd
>>> data = {'chrom': ['chr1', 'chr1', 'chr1'],
... 'first_bp_intron':[100, 100, 130], 'last_bp_intron':[180, 200, 200],
... 'unique_junction_reads':[90, 10, 40],
... 'multimap_junction_reads':[0, 0, 0]}
>>> sj = pd.DataFrame(data)
>>> get_psis(sj, min_multimap=0)
  chrom  first_bp_intron  last_bp_intron  multimap_junction_reads  \
0  chr1              100             180                        0
1  chr1              100             200                        0
2  chr1              130             200                        0
<BLANKLINE>
   unique_junction_reads  multimap_junction_reads_filtered  \
0                     90                                 0
1                     10                                 0
2                     40                                 0
<BLANKLINE>
   unique_junction_reads_filtered  total_filtered_reads  psi5  psi3
0                              90                    90   0.9   1.0
1                              10                    10   0.1   0.2
2                              40                    40   1.0   0.8
<BLANKLINE>
[3 rows x 10 columns]