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39 grep '>' nrf1_seq.fa | cut -f1 -d' '|cut -c 2
40 grep '>' nrf1_seq.fa | cut -f1 -d' '|cut -c 1
41 grep '>' nrf1_seq.fa | cut -f1 -d','
42 grep '>' nrf1_seq.fa | cut -f2 -d','
43 grep '>' nrf1_seq.fa | cut -f3 -d','
44 echo test
45 echo test >file1
46 ls
47 cat file1
48 echo test\n >file1
49 cat file1
50 echo test\ >file1
51 cat file1
52 ls
53 echo "Bioinformatics is great \n start writing scripts"
54 echo -e "Bioinformatics is great \n start writing scripts"
55 echo -e "Bioinformatics is great\n start writing scripts"
56 echo -e "Bioinformatics is great \nstart writing scripts"
57 man echo
58 echo -e "Bioinformatics is great \tstart writing scripts"
59 man echo
60 ls
61 ls \home
62 ls
63 ls /home/
64 ls
65 source activate icipe-env
66 ls
67 jupyter lab --no-browser
68 ls
69 jupyter lab --no-browser
70 ls
71 locate test
72 ls
73 cd EANBIT/
74 ls
75 cd Linux/Data/
76 ls
77 head nrf1_seq.fa
78 more nrf1_seq.fa
79 grep '>' nrf1_seq.fa
80 ls
81 cd
82 pwd
83 l
84 ls
85 cd EANBIT/
86 ls
87 cd Linux/
88 ls
89 cd Data/
90 ls
91 ls tmp/
92 cd tmp/PlasmoDB-9.0_Pfalciparum_BarcodeIsolates.fasta .
93 cp tmp/PlasmoDB-9.0_Pfalciparum_BarcodeIsolates.fasta .
94 ls
95 cd ..
96 ls
97 cd Python/
98 ls
99 mkdir Code
100 ls
101 cd Code/
102 ls
103 clone https://github.com/kipkurui/Python4Bioinformatics.git
104 git clone https://github.com/kipkurui/Python4Bioinformatics.git
105 ls
106 cd Python4Bioinformatics/
107 ls
108 cd Intro-to-Python/
109 ls
110 cd ..
111 ls
112 cd ..
113 ls
114 source activate icipe-env
115 jupyter lab --no-browser
116 cd EANBiT/
117 ls
118 cd Python/
119 lls
120 ls
121 cd Python
122 cd Python4Bioinfo/
123 ls
124 git status
125 ls
126 conda list
127 ls
128 cd miniconda3/
129 ls
130 cd bin/
131 ls
132 cd ..
133 ls
134 cd envs/
135 ls
136 cd icipe-env/
137 ls
138 cd bin/
139 ls
140 cd
141 ls
142 source activate icipe-env
143 sudo jupyter labhub
144 ls
145 exit
146 ls
147 source activate icipe-env
148 jupyter lab --no-browser
149 cd
150 ls
151 pwdd
152 pwd
153 python
154 ls
155 ls
156 cd EANBiT/
157 ls
158 cd Python/
159 ls
160 cd Python
161 cd Python4Bioinfo/
162 ls
163 git status
164 git add Intro-to-Python/00.ipynb
165 git add README.md
166 ls
167 git commit -m'updating installation instructions'
168 git push
169 ls
170 cd ../../../EANBIT/
171 ls
172 cd Python/
173 ls
174 cd Code/
175 ls
176 git fetch https://github.com/kipkurui/Python4Bioinformatics.git
177 git status
178 cd Python4Bioinformatics/
179 git status
180 git fetch
181 ls
182 git statu
183 git status
184 cd
185 cd EANBiT/
186 ls
187 cd Python/
188 ls
189 cd Python
190 cd Python4Bioinfo/
191 ls
192 git status
193 git add README.md
194 git commit -m'Further updates to installation'
195 git push
196 ls
197 cd ..
198 ls
199 cd Python4Bioinfo/
200 ls
201 git fetch
202 ls
203 pwd
204 cd ..
205 cd
206 cd EANBIT/
207 ls
208 cd Python/Code/Python4Bioinformatics/
209 ls
210 git status
211 git fetch
212 ls
213 python
214 python
215 source acctivate icipe-env
216 source activate icipe-env
217 jupyter lab --no-browser
218 conda list
219 source activate icipe-env
220 cd EANBIT/
221 jupyter lab --no-browser
222 ls
223 cd EANBiT/
224 ls
225 cd Python/
226 ls
227 source activate icipe-env
228 ls
229 jupyter lab --no-browser
230 ls
231 pwd
232 ls
233 pwd
234 cd EANBiT/
235 ls
236 cd Python/
237 ls
238 cd Python
239 cd Python4Bioinfo/
240 ls
241 git status
242 git add Intro-to-Python/00.ipynb
243 git add Intro-to-Python/01.ipynb
244 git add Intro-to-Python/02.ipynb
245 git add README.md
246 git status
247 git add Intro-to-Python/00.ipynb
248 git status
249 git commit -m'Harmonized instructions'
250 git push
251 ls
252 source activate icipe-env
253 ls
254 jupyter lab
255 jupyter lab --no-browser
256 exit
257 ls
258 source activate icipe-env
259 jupyter lab --no-browser
260 cd Obiero/
261 ls
262 conda install -c etetoolkit ete3 ete_toolchain
263 ete3 build check
264 l
265 ls
266 paml
267 ls
268 conda install -c bioconda paml
269 paml
270 codeml
271 ls
272 paml
273 ls
274 pamlm
275 paml
276 source activate icipe-env
277 jupyter lab --no-browser
278 ls
279 source activate icipe-env
280 jupyter lab --no-browser
281 ls
282 cd Obiero/
283 ls
284 wget https://www.ebi.ac.uk/Tools/services/rest/emboss_backtranseq/result/emboss_backtranseq-I20180617-152012-0807-33643867-p2m/out
285 ls
286 mv out
287 mv out A.compressa_annotated_ORs_nuc_bt.fasta
288 ls
289 modules
290 module
291 module list
292 module av
293 module load muscle
294 muscle --help
295 source activate icipe-env
296 ls
297 jupyter lab --no-browser
298 module load muscle
299 muscle --help
300 cd Obiero/
301 ls
302 muscle -in A.compressa_annotated_ORs_nuc_bt.fasta A.compressa_annotated_ORs_tree.fasta
303 muscle -in A.compressa_annotated_ORs_nuc_bt.fasta -out A.compressa_annotated_ORs_tree.fasta
304 ls
305 source activate icipe-env
306 jupyter lab --no-browser
307 ls
308 source activate icipe-env
309 mkdir Obiero
310 ls
311 jupyter lab --no-browser
312 AchameJeso@15
313 ls
314 source activate icipe-env
315 jupyter lab --no-brwser
316 jupyter lab --no-browser
317 ls
318 cd Obiero/
319 ls
320 module load muscle
321 muscle -in A.compressa_annotated_ORs_nuc_bt.fasta -out A.compressa_annotated_ORs_tree.fasta
322 ls
323 module av
324 source activate icipe-env
325 jupyter lab --no-browser
326 exit
327 ls
328 cd Obiero/
329 ls
330 mv A.compressa_annotated_ORs_tree.fasta A.compressa_annotated_ORs_aln.txt
331 mv A.compressa_annotated_ORs_tree2.fasta A.compressa_annotated_ORs_tree.txt
332 lsls
333 ls
334 mv A.compressa_annotated_ORs_tree2.txt A.compressa_annotated_ORs_tree.txt
335 ls
336 mv untitled.txt codeml.ctl
337 ls
338 ]
339 exit
340 ls
341 source activate icipe-env
342 jupyter lab --no-browser
343 exit
344 du -sh
345 myquota
346 top
347 cat /proc/meminfo
348 sinfo
349 sinfo -a
350 parallel
351 parallel -h
352 lshw
353 cat /proc/cpuinfo
354 exit
355 sudo
356 sudo apt-get install ls
357 sudo yum install ls
358 ls
359 cd
360 cd EANBiT/
361 ls
362 exit
363 ls
364 ls /home/
365 sudo useradd trainer1
366 sudo useradd -d /home/trainer1 -m trainer1
367 cd /home/trainer1/
368 sudo passwd trainer1
369 ls
370 cd /home/
371 ls
372 exit
373 ls
374 source activate py27
375 ls
376 cd Accreditation/RNASeq/Code/
377 ls
378 exit
379 test
380 ls
381 cd Accreditation/
382 ls
383 cd RNASeq/
384 ls
385 exit
386 move
387 exit
388 ls
389 cd Careen/QPhred_20/
390 ls
391 cp /tmp/QPhred_20/ ../
392 l
393 cd ..
394 ls
395 rm -r QPhred_20/
396 ls
397 cp /tmp/QPhred_20/ ./
398 cp -r /tmp/QPhred_20/ ./
399 ls
400 cd QPhred_20/
401 ls
402 less Lav1_1.fastq_trim_2.fq2.filt_Gmm.arf
403 cd ../BED/
404 ls
405 head Adfem2_Gmm_arf.bed
406 head Gmm_non_coding_annotated_tblout.bed
407 head Adfem2_Gmm_arf.bed
408 conda install -c bioconda cufflinks
409 tmux
410 exit
411 ls
412 cd Accreditation/
413 ls
414 cd RNASeq/
415 ls
416 cd Results/
417 ls
418 cd QC/
419 ls
420 python ../../Code/fastqc_summarizer.py
421 ls
422 cat all_mod_scores.csv
423 python ../../Code/fastqc_summarizer.py
424 ls
425 python ../../Code/fastqc_summarizer.py
426 conda install pandas
427 conda install seaborn
428 python ../../Code/fastqc_summarizer.py
429 ls
430 cd /opt/data/accreditation
431 ls
432 cd training/
433 ls
434 cd ../bin/
435 ls
436 cd ..
437 ls
438 cd training/\
439 ls
440 cd ..
441 ls
442 cd vowino/
443 ls
444 cd F16FTSEUHT0840_MONyxaR/
445 ls
446 cd clean_reads/
447 ls
448 cd Fastqc_stats/
449 ls
450 cd fastqc_aggregate.sh
451 cd fq_aggregated/
452 ls
453 cd adapter_content/
454 ls
455 cd ..
456 ls
457 cat statistics.txt
458 cat summary.txt
459 cd ..
460 ls
461 cd ..
462 ls
463 cd Tophat/
464 ls
465 cd ..
466 ls
467 cd 701-B12/
468 ls
469 cd ..
470 ;s
471 ls
472 cd ..
473 ls
474 cd 719-dataset/
475 ls
476 cd ..
477 ls
478 cd clean_reads/
479 ls
480 cd ..
481 ls
482 cd ..
483 ls
484 cd ..
485 ls
486 cd ingeno/
487 ls
488 cd accreditation/
489 ls
490 cd training/
491 ls
492 cat script.sh
493 ls
494 cd seqs/
495 ls
496 cd fastqs/
497 ls
498 cd ../..
499 ls
500 cat out.txt
501 cd
502 ls
503 cd Accreditation/
504 ls
505 cd RNASeq/
506 ls
507 cd Code/
508 ls
509 ./run_qc.sh
510 cd ../Data/
511 ls
512 mkdir hg38
513 cd hg38/
514 lws
515 ls
516 wget ftp://ftp.ensembl.org/pub/release-92/gtf/homo_sapiens/Homo_sapiens.GRCh38.92.gtf.gz
517 ls
518 wget ftp://ftp.ensembl.org/pub/release-92/gff3/homo_sapiens/Homo_sapiens.GRCh38.92.chr.gff3.gz
519 wget ftp://ftp.ensembl.org/pub/release-92/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
520 ls
521 L
522 cd /etc/opt
523 ls
524 cd /etc/
525 ls
526 cd
527 cd /tmp/
528 ls
529 mkdir Careen
530 ls
531 cd
532 mkdir Careen
533 ls
534 cd Careen/
535 ls
536 cp -r /tmp/QPhred_20/ ./
537 ls
538 cd QPhred_20/
539 ls
540 head Adfem2_1.fastq_trim_2.fq2.filt_2.fa
541 ls
542 cd ..
543 ls
544 rename
545 man rename
546 ls
547 cd /tmp/QPhred_20/
548 ls
549 less Glossina-morsitans-Yale_SCAFFOLDS_GmorY1.fasta.tblout
550 less Glossina-morsitans-Yale_SCAFFOLDS_GmorY1.fasta.cmscan
551 less Glossina-morsitans-Yale_SCAFFOLDS_GmorY1.fasta.tblout
552 cut -f2
553 cut -f2
554 cut -f2 Glossina-morsitans-Yale_SCAFFOLDS_GmorY1.fasta.tblout |head
555 cut -f2 -d" " Glossina-morsitans-Yale_SCAFFOLDS_GmorY1.fasta.tblout |head
556 cut -f4 -d" " Glossina-morsitans-Yale_SCAFFOLDS_GmorY1.fasta.tblout |head
557 tail -n 23 Glossina-morsitans-Yale_SCAFFOLDS_GmorY1.fasta.tblout |head
558 tail -n 23 Glossina-morsitans-Yale_SCAFFOLDS_GmorY1.fasta.tblout |cut -f2
559 tail -n 23 Glossina-morsitans-Yale_SCAFFOLDS_GmorY1.fasta.tblout |cut -f21
560 tail -n 23 Glossina-morsitans-Yale_SCAFFOLDS_GmorY1.fasta.tblout |cut -f2 -d" "
561 tail -n 23 Glossina-morsitans-Yale_SCAFFOLDS_GmorY1.fasta.tblout |cut -f4 -d" "
562 tail -n 23 Glossina-morsitans-Yale_SCAFFOLDS_GmorY1.fasta.tblout |cut -f6 -d" "
563 tail -n 23 Glossina-morsitans-Yale_SCAFFOLDS_GmorY1.fasta.tblout
564 less Glossina-morsitans-Yale_SCAFFOLDS_GmorY1.fasta.tblout
565 cut -f1 Glossina-morsitans-Yale_SCAFFOLDS_GmorY1.fasta.tblout
566 head -100 Glossina-morsitans-Yale_SCAFFOLDS_GmorY1.fasta.tblout |cut -f2
567 head -100 Glossina-morsitans-Yale_SCAFFOLDS_GmorY1.fasta.tblout |cut -f2 -d" "
568 head -100 Glossina-morsitans-Yale_SCAFFOLDS_GmorY1.fasta.tblout |cut -f3 -d" "
569 head -100 Glossina-morsitans-Yale_SCAFFOLDS_GmorY1.fasta.tblout |cut -f12 -d" "
570 head -100 Glossina-morsitans-Yale_SCAFFOLDS_GmorY1.fasta.tblout |cut -f5 -d" "
571 head -100 Glossina-morsitans-Yale_SCAFFOLDS_GmorY1.fasta.tblout |cut -f6 -d" "
572 head -100 Glossina-morsitans-Yale_SCAFFOLDS_GmorY1.fasta.tblout |cut -f7 -d" "
573 head -100 Glossina-morsitans-Yale_SCAFFOLDS_GmorY1.fasta.tblout |cut -f9 -d" "
574 head -100 Glossina-morsitans-Yale_SCAFFOLDS_GmorY1.fasta.tblout |cut -f1 -d" "
575 head -100 Glossina-morsitans-Yale_SCAFFOLDS_GmorY1.fasta.tblout
576 head -100 Glossina-morsitans-Yale_SCAFFOLDS_GmorY1.fasta.tblout |cut -f5 -d" "
577 head -100 Glossina-morsitans-Yale_SCAFFOLDS_GmorY1.fasta.tblout |cut -f10 -d" "
578 head -100 Glossina-morsitans-Yale_SCAFFOLDS_GmorY1.fasta.tblout |cut -f11 -d" "
579 ls
580 less Lav1_1.fastq_trim_2.fq2.filt_2.arf
581 cut -f2 Lav1_1.fastq_trim_2.fq2.filt_2.arf |head
582 cut -f1 Lav1_1.fastq_trim_2.fq2.filt_2.arf |head
583 cut -f4 Lav1_1.fastq_trim_2.fq2.filt_2.arf |head
584 cut -f6 Lav1_1.fastq_trim_2.fq2.filt_2.arf |head
585 cut -f6,7 Lav1_1.fastq_trim_2.fq2.filt_2.arf |head
586 cut -f6,9 Lav1_1.fastq_trim_2.fq2.filt_2.arf |head
587 cut -f6,8,9 Lav1_1.fastq_trim_2.fq2.filt_2.arf |head
588 cut -f6,8,9,7 Lav1_1.fastq_trim_2.fq2.filt_2.arf |head
589 man cut
590 cd
591 cd Accreditation/
592 ls
593 cd RNASeq/
594 ls
595 cd Results/
596 ls
597 cd Trim_QC/
598 ls
599 python ../../Code/fastqc_summarizer.py
600 ls
601 cd ..
602 ls
603 rm sample37_R1_*
604 ls
605 rm -r sample37_R1_*
606 ls
607 cd ../Data/
608 ls
609 mkdir test
610 ls
611 rmdir test/
612 ls
613 mkdir Practice
614 ls
615 mv sample* Practice/
616 ls
617 mv practice.dataset.metadata.tsv Practice/
618 ls
619 cd hg38/
620 ls
621 gunzip Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
622 ls
623 gunzip Homo_sapiens.GRCh38.92.chr.gff3.gz
624 ls
625 cd ../../Code/
626 ls
627 mv Homo_sapiens.GRCh38.dna.primary_assembly.* ../Data/hg38/
628 ls
629 conda install -c bioconda tophat
630 module load tophat
631 tophat
632 module load tophat2/2.1.1
633 module load tophat2
634 tophat
635 conda create -n py27 python=2.7
636 conda activate py27
637 ls
638 tmux
639 cd
640 cd Careen/
641 ls
642 cd QPhred_20/
643 ls
644 Glossina-morsitans-Yale_SCAFFOLDS_GmorY1.fasta.tblout
645 ls -a
646 ls -l
647 ls
648 cd
649 ls
650 \cd Careen/QPhred_20/
651 ls
652 ls -l
653 clear
654 cd ..
655 ls
656 cd BED/
657 ls
658 conda install -c bioconda pybedtools
659 bedtools
660 bedtools intersect
661 bedtools intersect Adfem2_Gmm_arf.bed Gmm_non_coding_annotated_tblout.bed |head
662 bedtools intersect
663 bedtools intersect -a Adfem2_Gmm_arf.bed -b Gmm_non_coding_annotated_tblout.bed |head
664 bedtools intersect -a Adfem2_Gmm_arf.bed -b Gmm_non_coding_annotated_tblout.bed |wc -l
665 wc -l Adfem2_Gmm_arf.bed
666 wc -l Gmm_non_coding_annotated_tblout.bed
667 ls
668 ls -l
669 bedtools intersect -a Adfem2_Gmm_arf.bed -b Gmm_non_coding_annotated_tblout.bed |wc -l
670 cat -t Gmm_non_coding_annotated_tblout.bed
671 cat -t Gmm_non_coding_annotated_tblout.bed |head
672 cat -t Adfem2_Gmm_arf.bed | head
673 bedtools intersect -a Adfem2_Gmm_arf.bed -b Gmm.bed |wc -l
674 ls
675 cut -f1,2,3 Gmm.bed >Gmm_2.bed
676 ls
677 bedtools intersect -a Adfem2_Gmm_arf.bed -b Gmm_2.bed |wc -l
678 bed12ToBed6 Gmm_2.bed |head
679 bed12ToBed6 -n Gmm_2.bed |head
680 bed12ToBed6 -n -i Gmm_2.bed |head
681 ls
682 bed12ToBed6 -n -i test.bed |head
683 bedtools intersect -a Adfem2_Gmm_arf.bed -b test.bed |wc -l
684 bedtools intersect -a Adfem2_Gmm_arf.bed -b test.bed |head
685 bedtools intersect -a test.bed -b Adfem2_Gmm_arf.bed |head
686 bedtools intersect -a test.bed -b Adfem2_Gmm_arf.bed |wc -l
687 bedtools intersect -wa -a test.bed -b Adfem2_Gmm_arf.bed |wc -l
688 bedtools intersect -wb -a test.bed -b Adfem2_Gmm_arf.bed |wc -l
689 bedtools intersect -wb -a test.bed -b Adfem2_Gmm_arf.bed
690 bedtools intersect -wb -a test.bed -b Adfem2_Gmm_arf.bed |head
691 bedtools intersect -wa -a test.bed -b Adfem2_Gmm_arf.bed |head
692 bedtools intersect -wa -v -a test.bed -b Adfem2_Gmm_arf.bed |wc -l
693 bedtools intersect -wb -v -a test.bed -b Adfem2_Gmm_arf.bed |wc -l
694 bedtools intersect -v -a test.bed -b Adfem2_Gmm_arf.bed |wc -l
695 bedtools intersect -v -a Adfem2_Gmm_arf.bed -b test.bed |wc -l
696 bedtools intersect -a Adfem2_Gmm_arf.bed -b test.bed |wc -l
697 wc -l Adfem2_Gmm_arf.bed
698 bedtools intersect -a Adfem2_Gmm_arf.bed -b test.bed |head
699 bedtools intersect -wo -a Adfem2_Gmm_arf.bed -b test.bed |head
700 bedtools intersect -wo -a Adfem2_Gmm_arf.bed -b test.bed |less
701 exit
702 cd Accreditation/RNASeq/Code/
703 ls
704 conda install -c bioconda tophat
705 ls
706 cp fastqc_summarizer.py /tmp/QPhred_20/
707 cp fastqc_summarizer.py /tmp
708 ls
709 cd ../Results/Trim_QC/
710 ls
711 source activate py27
712 jupyter lab --no-browser
713 conda install jupyter
714 jupyter lab --no-browser
715 conda install -c conda-forge jupyterlab
716 jupyter lab --no-browser
717 exit
718 ls
719 echo 79BD311D && /usr/bin/env && echo CB903F36
720 cd Accreditation/
721 ls
722 cd RNASeq/
723 ls
724 cd Code/
725 ls
726 echo 11FE0769 && /usr/bin/env && echo 7657F06B
727 ls
728 echo 11FE0769 && /usr/bin/env && echo 7657F06B
729 source activate py27
730 jupyter lab
731 o9& urbnev && echo 7657F06B
732 l
733 echo 11FE0769 && /usr/bin/env && echo 7657F06B
734 Bexqqqquit
735 uit echo 11FE0769 && /usr/bin/env && echo 7657F06B
736 echo 11FE0769 && /usr/bin/env && echo 7657F06B
737 ls
738 cd Accreditation/
739 cd RNASeq/
740 ls
741 cd Results/
742 ls
743 cd Cufflinks/
744 ls
745 cd sample
746 cd sample37
747 ls
748 cd ..
749 ls
750 cd sample40
751 ls
752 cd ..
753 ls
754 cd ..
755 ls
756 cd TopHat/
757 ls
758 cd sample37
759 ls
760 cd
761 tmux -h
762 man tmux
763 source activate py27
764 jupyter lab --no-browser
765 ls
766 cd Accreditation/
767 ls
768 cd RNASeq/
769 ls
770 exi
771 exit
772 source activate iccipe-env
773 source activate icipe-env
774 jupyter lab --no-browser
775 ls
776 cd EANBiT/
777 ls
778 cd Python/
779 ls
780 cd Python
781 cd Python4Bioinfo/
782 ls
783 git status
784 git checkout training
785 git status
786 git merge master
787 git status
788 git log
789 git revert HEAD
790 ls
791 cd Intro-to-Python/
792 ls
793 cd ..
794 ls
795 git pull
796 ls
797 git merge --abort
798 git status
799 cd Intro-to-Python/
800 ls
801 git checkout master
802 git merge training
803 git status
804 git commit
805 git add ../README.md
806 git commit
807 git status
808 ls
809 cd ..
810 ls
811 git status
812 git push
813 ls
814 git chekout training
815 git checkout training
816 ls
817 cd Intro-to-Python/
818 ls
819 cd ..
820 ls
821 cd Intro-to-Python/
822 ls
823 cp 03.ipynb ../../
824 ls
825 cd ..
826 ls
827 cd ..
828 ls
829 cd Python
830 cd Python4Bioinfo/
831 ls
832 cp -r Intro-to-Python/ ../../
833 ls
834 cd ..
835 ls
836 cd ..
837 ls
838 cd Intro-to-Python/
839 ls
840 git status
841 cd ..
842 cd Python/
843 cd Python4Bioinfo/
844 ls
845 git status
846 git checkout master
847 ls
848 cd Careen/BED/
849 ls
850 modules av
851 modules -av
852 modules avail
853 module avail
854 module av
855 ls
856 cd ..
857 ls
858 cp -r BED/ /tmp/
859 ls
860 cd /tmp/
861 ls
862 cd BED/
863 ls
864 cd
865 cd Accreditation/
866 ls
867 cd RNASeq/
868 ls
869 cd Results/
870 ls
871 mkdir Cufflinks
872 ols
873 ls
874 cd ../Data/
875 ls
876 cd p
877 cd Practice/
878 ls
879 ls |grep 'sample'
880 ls |grep 'sample'|cut -f1 -d'_'
881 ls |grep 'sample'|cut -f1 -d'_'|uniq
882 ls |grep 'sample'|cut -f1 -d'_'|uniq >../../Code/samples
883 ls
884 cd
885 cd Accreditation/RNASeq/Code/
886 ls
887 chmod +x run_tophat.sh
888 cat run_tophat.sh
889 ls
890 c
891 ./run_
892 ./run_tophat.sh
893 ls
894 which python
895 cd
896 cd EANBiT/
897 ls
898 cd Python/
899 ls
900 cd Python4Bioinfo/
901 cd ..
902 ls
903 mv Python.pdf ../
904 ls
905 cd Python4Bioinfo/
906 ls
907 git status
908 ls
909 cd ../
910 ls
911 cd ..
912 ls
913 cd Intro-to-Python/
914 ls
915 cp 04.ipynb ../Python/Python4Bioinfo/Intro-to-Python/
916 ls
917 cd ../Python/Python4Bioinfo/
918 git status
919 git add Intro-to-Python/03.ipynb Intro-to-Python/execution.png
920 git commit -m'Adding Data structures notes'
921 git push
922 git status
923 git add Intro-to-Python/04.ipynb
924 git commit -m'Dictionaries Notebook'
925 git push
926 ls
927 cp ../../Intro-to-Python/05.ipynb ./Intro-to-Python/
928 ls
929 git status
930 git add Intro-to-Python/04.ipynb
931 git add Intro-to-Python/05.ipynb
932 git commit -m'Adding notes for conditionals'
933 git push
934 ls
935 ls ../../Intro-to-Python/
936 cp ../../Intro-to-Python/06.ipynb Intro-to-Python/
937 ls Intro-to-Python/
938 ls
939 git status
940 git add Intro-to-Python/06.ipynb
941 git commit -m"Adding the functions notebook"
942 git push
943 git status
944 git add Intro-to-Python/06.ipynb
945 git commit -m"Updating the functions notebook"
946 git push
947 ls
948 git status
949 git add Files/
950 git add Intro-to-Python/0*
951 git status
952 git add Intro-to-Python/*.py
953 git status
954 git add Intro-to-Python/08.ipynb
955 ls
956 git commit -m"File, Scripts and modules'
957 "
958 git push
959 ls
960 git status
961 ls
962 git status
963 git add Intro-to-Python/0*
964 git status
965 git add README.md
966 git commit -m"Adding Pands and Bioinformatics Notebooks"
967 git push
968 git status
969 git add Intro-to-Python/00.ipynb
970 git add README.md
971 git commit -m'minor edits'
972 git push
973 ed
974 man ed
975 man sed
976 exit
977 cd Accreditation/RNASeq/Code/
978 ls
979 source activate py27
980 ls
981 ./run_tophat.sh
982 exit
983 ls
984 source activate py27
985 conda install -c bioconda cufflinks
986 exit
987 tmux
988 tmux new -s accredit
989 exit
990 ls
991 mkdir MARS
992 ls
993 source activate icipe-env
994 jupyter lab --no-browser
995 exiit
996 exit
997 cd EANBIT/
998 ls
999 cd Linux/
1000 ls
1001 cd Data/
1002 ls
1003 grep -m18 nrf1_seq.fa
1004 grep -m18 '>' nrf1_seq.fa
1005 grep -m18 '>' nrf1_seq.fa |wc -l
1006 man grep
1007 grep -m18 -n '>' nrf1_seq.fa |wc -l
1008 grep -m18 -n '>' nrf1_seq.fa
1009 grep -m19 -n '>' nrf1_seq.fa
1010 grep -m19 -n '>' nrf1_seq.fa|tail -n2
1011 grep -m19 -n '>' nrf1_seq.fa|tail 2
1012 grep -m19 -n '>' nrf1_seq.fa|tail -n 2
1013 grep -m19 -n '>' nrf1_seq.fa|tail -n 2|cut -f1 -d":"
1014 head -n 3445 nrf1_seq.fa |tail -n -794
1015 head -n 3445 nrf1_seq.fa |tail -n -793
1016 head -n 3444 nrf1_seq.fa |tail -n -794
1017 head -n 3444 nrf1_seq.fa |tail -n -794 |wc -c
1018 grep -m19 -n '>' nrf1_seq.fa|tail -n 2|cut -f1 -d":"
1019 grep -m19 -n '>' nrf1_seq.fa|tail -n 1|cut -f1 -d":"
1020 last=grep -m19 -n '>' nrf1_seq.fa|tail -n 1|cut -f1 -d":"
1021 last=expr `grep -m19 -n '>' nrf1_seq.fa|tail -n 1|cut -f1 -d":"`
1022 `grep -m19 -n '>' nrf1_seq.fa|tail -n 1|cut -f1 -d":"`
1023 head -n `grep -m19 -n '>' nrf1_seq.fa|tail -n 1 | cut -f1 -d":"` nrf1_seq.fa |tail -n -`grep -m19 -n '>' nrf1_seq.fa|head -n 1 |cut -f1 -d":"` |wc -c
1024 head -n `grep -m19 -n '>' nrf1_seq.fa|tail -n 1 | cut -f1 -d":"` nrf1_seq.fa |tail -n -`grep -m19 -n '>' nrf1_seq.fa|head -n 1 |cut -f1 -d":"`
1025 head -n `grep -m19 -n '>' nrf1_seq.fa|tail -n 1 | cut -f1 -d":"` nrf1_seq.fa |tail -n -`grep -m19 -n '>' nrf1_seq.fa|head -n 2 |cut -f1 -d":"`
1026 head -n `grep -m19 -n '>' nrf1_seq.fa|tail -n 1 | cut -f1 -d":"` nrf1_seq.fa |tail -n - `grep -m19 -n '>' nrf1_seq.fa|head -n 2 |cut -f1 -d":"`
1027 head -n `grep -m19 -n '>' nrf1_seq.fa|tail -n 1 | cut -f1 -d":"` nrf1_seq.fa |tail -n - `grep -m19 -n '>' nrf1_seq.fa|head -n 1 |cut -f1 -d":"`
1028 head -n `grep -m19 -n '>' nrf1_seq.fa|tail -n 1 | cut -f1 -d":"` nrf1_seq.fa |tail -n -`grep -m19 -n '>' nrf1_seq.fa|head -n 1 |cut -f1 -d":"` |wc -c
1029* head -n `grep -m19 -n '>' nrf1_seq.fa|tail -n 1 | cut -f1 -d":"` nrf1_seq.fa |tail -n -`grep -m19 -n '>' nrf1_seq.fa|head -n 1 |cut -f
1030 grep -m19 -n '>' nrf1_seq.fa|head -n 1 |cut -f1 -d":"
1031 grep -m19 -n '>' nrf1_seq.fa|head -n 1
1032 head nrf1_seq.fa
1033 grep -m19 -n '>' nrf1_seq.fa|head -n 1
1034 grep -m19 -n '>' nrf1_seq.fa
1035 grep -m19 -n '>' nrf1_seq.fa|tail -n 2
1036 grep -m19 -n '>' nrf1_seq.fa|tail -n 2|head -1
1037 head -n `grep -m19 -n '>' nrf1_seq.fa|tail -n 1 | cut -f1 -d":"` nrf1_seq.fa |tail -n -`grep -m19 -n '>' nrf1_seq.fa|tail -n 2| head -n 1 |cut -f1 -d":"` |wc -c
1038 history >history