| seqid | Name | ||
|---|---|---|---|
| 5 | Transcript_10 | EDO31303 | |
| 9 | Transcript_100 | EDO42116 | |
| 19 | Transcript_101 | EDO42087 | |
| 24 | Transcript_102 | EDO43514 | |
| 39 | Transcript_103 | tr|A7SUP6|A7SUP6_NEMVE Predicted protein OS=Nematostella vectensis OX=45351 GN=v1g217764 PE=4 SV=1 | |
| 58 | Transcript_105 | EDO33432 | |
| 60 | Transcript_107 | tr|A7S0C0|A7S0C0_NEMVE Predicted protein OS=Nematostella vectensis OX=45351 GN=v1g184098 PE=4 SV=1 | |
| 61 | Transcript_109 | EDO49229 | |
| 71 | Transcript_11 | tr|A7RQ19|A7RQ19_NEMVE Predicted protein OS=Nematostella vectensis OX=45351 GN=v1g239897 PE=4 SV=1 |
| >hairpin_1_fwd | |
| GATCGGAAGAGCACACGTCTGAACTCCAGTC | |
| >hairpin_1_revcomp | |
| GACTGGAGTTCAGACGTGTGCTCTTCCGATC | |
| >hairpin_2_fwd | |
| ACACTCTTTCCCTACACGACGCTCTTCCGATC | |
| >hairpin_2_revcomp | |
| GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT | |
| >Illumina_top | |
| ACACTCTTTCCCTACACGACGCTCTTCCGATC |
| ########################################## | |
| ## 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 |
| # 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)))] |
Got this error message:
[ljcohen@dev-intel16 Porites_astreoites_larvae_salinity]$ git push origin master
error: The requested URL returned error: 403 Forbidden while accessing https://github.com/ljcohen/Porites_astreoites_larvae_salinity.git/info/refs
fatal: HTTP request failed
Googled problem and found this:
| ################################################################### | |
| """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 |
| import screed | |
| import os | |
| from os import path | |
| import subprocess | |
| from subprocess import Popen, PIPE | |
| def make_dir(dirname): | |
| if os.path.isdir(dirname) == False: | |
| os.mkdir(dirname) | |
| print("Directory created:", dirname) |
| #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 |
| >DNA_CS | |
| GCCATCAGATTGTGTTTGTTAGTCGCTTTTTTTTTTTGGAATTTTTTTTTTGGAATTTTTTTTTTGCGCTAACAACCTCCTGCCGTTTTGCCCGTGCATATCGGTCACGAACAAATCTGATTACTAAACACAGTAGCCTGGATTTGTTCTATCAGTAATCGACCTTATTCCTAATTAAATAGAGCAAATCCCCTTATTGGGGGTAAGACATGAAGATGCCAGAAAAACATGACCTGTTGGCCGCCATTCTCGCGGCAAAGGAACAAGGCATCGGGGCAATCCTTGCGTTTGCAATGGCGTACCTTCGCGGCAGATATAATGGCGGTGCGTTTACAAAAACAGTAATCGACGCAACGATGTGCGCCATTATCGCCTAGTTCATTCGTGACCTTCTCGACTTCGCCGGACTAAGTAGCAATCTCGCTTATATAACGAGCGTGTTTATCGGCTACATCGGTACTGACTCGATTGGTTCGCTTATCAAACGCTTCGCTGCTAAAAAAGCCGGAGTAGAAGATGGTAGAAATCAATAATCAACGTAAGGCGTTCCTCGATATGCTGGCGTGGTCGGAGGGAACTGATAACGGACGTCAGAAAACCAGAAATCATGGTTATGACGTCATTGTAGGCGGAGAGCTATTTACTGATTACTCCGATCACCCTCGCAAACTTGTCACGCTAAACCCAAAACTCAAATCAACAGGCGCCGGACGCTACCAGCTTCTTTCCCGTTGGTGGGATGCCTACCGCAAGCAGCTTGGCCTGAAAGACTTCTCTCCGAAAAGTCAGGACGCTGTGGCATTGCAGCAGATTAAGGAGCGTGGCGCTTTACCTATGATTGATCGTGGTGATATCCGTCAGGCAATCGACCGTTGCAGCAATATCTGGGCTTCACTGCCGGGCGCTGGTTATGGTCAGTTCGAGCATAAGGCTGACAGCCTGATTGCAAAATTCAAAGAAGCGGGCGGAACGGTCAGAGAGATTGATGTATGAGCAGAGTCACCGCGATTATCTCC |