johnsolk

johnsolk

>hairpin_1_fwd
GATCGGAAGAGCACACGTCTGAACTCCAGTC
>hairpin_1_revcomp
GACTGGAGTTCAGACGTGTGCTCTTCCGATC
>hairpin_2_fwd
ACACTCTTTCCCTACACGACGCTCTTCCGATC
>hairpin_2_revcomp
GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
>Illumina_top
ACACTCTTTCCCTACACGACGCTCTTCCGATC

johnsolk

##########################################
## Intersect and Venn Diagram Functions ##
##########################################
## Author: Thomas Girke
## Last update: August 15, 2009
## Utilities: 
## (1) Venn Intersects
##     Computation of Venn intersects among 2-20 or more sample sets using the typical
##     'only in' intersect logic of Venn comparisons, such as: objects present only in 
##     set A, objects present only in the intersect of A & B, etc. Due to this restrictive 

johnsolk

# custom script by Igor Dolgolev at NYUMC


plotPCAWithSampleNames = function(x, intgroup="condition", ntop=500)
{
  library("genefilter")
  library("lattice")
  
  rv = rowVars(assay(x))
  select = order(rv, decreasing=TRUE)[seq_len(min(ntop, length(rv)))]

johnsolk

###################################################################
"""Function: Take in a dammit gff3, dammit fasta, dammit namemap.
Output gff3 and fasta with trinity names.
by Dr. Tessa Pierce
"""
###################################################################

import sys
import os
import argparse

johnsolk

#outputs top 20 barcodes in file, if there are any
zcat lane1_sample_L001_R1_001.fastq.gz | head -400000 | grep '^@HWI' | cut -d : -f 10 | sort | uniq -c | sort -nr | head -20

johnsolk

johnsolk

johnsolk

>DNA_CS
GCCATCAGATTGTGTTTGTTAGTCGCTTTTTTTTTTTGGAATTTTTTTTTTGGAATTTTTTTTTTGCGCTAACAACCTCCTGCCGTTTTGCCCGTGCATATCGGTCACGAACAAATCTGATTACTAAACACAGTAGCCTGGATTTGTTCTATCAGTAATCGACCTTATTCCTAATTAAATAGAGCAAATCCCCTTATTGGGGGTAAGACATGAAGATGCCAGAAAAACATGACCTGTTGGCCGCCATTCTCGCGGCAAAGGAACAAGGCATCGGGGCAATCCTTGCGTTTGCAATGGCGTACCTTCGCGGCAGATATAATGGCGGTGCGTTTACAAAAACAGTAATCGACGCAACGATGTGCGCCATTATCGCCTAGTTCATTCGTGACCTTCTCGACTTCGCCGGACTAAGTAGCAATCTCGCTTATATAACGAGCGTGTTTATCGGCTACATCGGTACTGACTCGATTGGTTCGCTTATCAAACGCTTCGCTGCTAAAAAAGCCGGAGTAGAAGATGGTAGAAATCAATAATCAACGTAAGGCGTTCCTCGATATGCTGGCGTGGTCGGAGGGAACTGATAACGGACGTCAGAAAACCAGAAATCATGGTTATGACGTCATTGTAGGCGGAGAGCTATTTACTGATTACTCCGATCACCCTCGCAAACTTGTCACGCTAAACCCAAAACTCAAATCAACAGGCGCCGGACGCTACCAGCTTCTTTCCCGTTGGTGGGATGCCTACCGCAAGCAGCTTGGCCTGAAAGACTTCTCTCCGAAAAGTCAGGACGCTGTGGCATTGCAGCAGATTAAGGAGCGTGGCGCTTTACCTATGATTGATCGTGGTGATATCCGTCAGGCAATCGACCGTTGCAGCAATATCTGGGCTTCACTGCCGGGCGCTGGTTATGGTCAGTTCGAGCATAAGGCTGACAGCCTGATTGCAAAATTCAAAGAAGCGGGCGGAACGGTCAGAGAGATTGATGTATGAGCAGAGTCACCGCGATTATCTCC

johnsolk