ecwheele

-rwxrwxr-x 1 ecwheele yeo-group 3.8M Apr  8 19:09 miso/K562_WT_1/A3SS/summary/A3SS.miso_summary
-rwxrwxr-x 1 ecwheele yeo-group 2.6M Apr  8 19:14 miso/K562_WT_1/A5SS/summary/A5SS.miso_summary
-rwxrwxr-x 1 ecwheele yeo-group 3.8M Apr  8 18:42 miso/K562_WT_1/AFE/summary/AFE.miso_summary
-rwxrwxr-x 1 ecwheele yeo-group 1.8M Apr  8 19:01 miso/K562_WT_1/ALE/summary/ALE.miso_summary
-rwxrwxr-x 1 ecwheele yeo-group 4.6M Apr  8 18:00 miso/K562_WT_1/MXE/summary/MXE.miso_summary
-rwxrwxr-x 1 ecwheele yeo-group 1.6M Apr  8 19:18 miso/K562_WT_1/RI/summary/RI.miso_summary
-rwxrwxr-x 1 ecwheele yeo-group  17M Apr  8 17:55 miso/K562_WT_1/SE/summary/SE.miso_summary
-rwxrwxr-x 1 ecwheele yeo-group 597K Apr  8 19:21 miso/K562_WT_1/TANDEMUTR/summary/TANDEMUTR.miso_summary
-rwxrwxr-x 1 ecwheele yeo-group 3.4M Aug 10 13:15 miso/K562_WT_2/A3SS/summary/A3SS.miso_summary
-rwxrwxr-x 1 ecwheele yeo-group 2.4M Aug 10 13:23 miso/K562_WT_2/A5SS/summary/A5SS.miso_summary

ecwheele

sns.set_style('white')
plt.figure(figsize=(10,20))
ax1 = plt.subplot2grid((3,1),(0,0), title = 'Total Number of Differenitally Expressed Genes')
sns.barplot(x = 'count', y = 'sample', data = all_counts,hue = 'protein', palette ='deep',ax=ax1)

ecwheele

[ecwheele@tscc-login1 mds_splicing_v4]$ bash process_rnaseq.sh 
INFO  09:21:27,273 QScriptManager - Compiling 1 QScript 
INFO  09:21:36,790 QScriptManager - Compilation complete 
INFO  09:21:36,952 HelpFormatter - ---------------------------------------------------------------------- 
INFO  09:21:36,953 HelpFormatter - Queue v2.3-1155-g931452b, Compiled 2016/01/11 23:38:39 
INFO  09:21:36,953 HelpFormatter - Copyright (c) 2012 The Broad Institute 
INFO  09:21:36,953 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk 
INFO  09:21:36,954 HelpFormatter - Program Args: -S /home/ecwheele/gscripts/qscripts/analyze_rna_seq.scala --input manifest.txt --adapter TCGTATGCCGTCTTCTGCTTG --adapter ATCTCGTATGCCGTCTTCTGCTTG --adapter CGACAGGTTCAGAGTTCTACAGTCCGACGATC --adapter GATCGGAAGAGCACACGTCTGAACTCCAGTCAC -qsub -jobQueue home-scrm -log mds_splicing_v4.log --location /oasis/tscc/scratch/ecwheele/mds_splicing_v4/ --strict -keepIntermediates --flipped flip -run 
INFO  09:21:36,954 HelpFor

ecwheele

(ecwheele)[ecwheele@tscc-login1 clipper]$ python setup.py install

Installed /home/ecwheele/software/clipper/.eggs/setuptools_git-1.1-py3.5.egg
running install
running bdist_egg
running egg_info
writing top-level names to clipper.egg-info/top_level.txt
writing entry points to clipper.egg-info/entry_points.txt
writing clipper.egg-info/PKG-INFO
writing requirements to clipper.egg-info/requires.txt

ecwheele

fout = open('/home/ecwheele/data/analysis/clip/region_annotations_basic/basic_first_exons.bed','w')
for transcript in v19_basic_db.features_of_type('transcript'):
    reversers = transcript.strand == '-'
    for i, exon in enumerate(v19_basic_db.children(transcript, featuretype="exon")):
        if exon.strand == "+":
            if exon.start == transcript.start:
                line = '%s\t%s\t%s\t%s\t%s\t%s\n' % (exon.chrom,exon.start-1,exon.stop,exon.id,exon.score,exon.strand)
                fout.write(line)
            else:
                continue

ecwheele

#!/bin/env python

from __future__ import print_function
from __future__ import division
from future.utils import raise_with_traceback
import kvector
from argparse import ArgumentParser
import pandas as pd
import numpy as np
import os

ecwheele

#!/bin/env python

import pybedtools
import subprocess
from argparse import ArgumentParser
import os

#Todo: Need to add a check to see if the shuffled bed file already exists

ecwheele

outrigger index --sj-out-tab ../ep-cj-n2-ndiff-hs_S1_R1_001.polyATrim.adapterTrim.rmRep.bamSJ.out.tab --gtf /projeyeolab/genomes/hg19/gencode_v19/gencode.v19.annotation.gtf
2017-04-13 16:51:57     Creating folder ./outrigger_output ...
2017-04-13 16:51:57             Done.
2017-04-13 16:51:57     Creating folder ./outrigger_output/index ...
2017-04-13 16:51:57             Done.
2017-04-13 16:51:57     Creating folder ./outrigger_output/index/gtf ...
2017-04-13 16:51:57             Done.
2017-04-13 16:51:57     Creating folder ./outrigger_output/junctions ...
2017-04-13 16:51:57             Done.
2017-04-13 16:51:57     Found compiled junction reads file in ./outrigger_output/junctions/reads.csv and reading it in ...

ecwheele

ecwheele

**Array Jobs on TSCC**

We can specify in the submission parameters that we want to submit an array job. Here is an example. Notice the -t flag, that tells TSCC to use an array job to process this. Since we have 4 commands here, we will use -t 1-4.

    #!/bin/bash
    #PBS -N run_homer
    #PBS -o run_homer.sh.out
    #PBS -e run_homer.sh.err
    #PBS -l walltime=5:00:00
    #PBS -l nodes=1:ppn=1