Prunus yedoensis whole genome assembly
Library:
- total RNA, Illumina's TruSeq library kit
raw data:
PE:
MiSeq 500bp (library name: Prunus-1)
NextSeq 300bp (library name: Prunus-2)
MP:
NextSeq 3kb, 5kb, 10kbp, 15kb
File List:
PE:
[goonbokim@R820 miseq_genome_raw_fastq-gunzip]$ ll -h
total 153G
-rw-r--r-- 1 root root 138K Sep 15 14:36 140704_FASTQ.pdf
-rw-r--r-- 1 root root 212 Sep 15 14:36 140704_FASTQ.pdf.md5sum.txt
-rw-r--r-- 1 root root 217 Sep 15 14:40 check_md5sum.txt
-rw-r--r-- 1 root root 657 Sep 15 14:40 get_raw_fastq.pl
-rw-r--r-- 1 root root 248 Sep 15 14:40 get_url.txt
-rw------- 1 root root 78M Sep 15 14:40 nohup.out
-rw-r--r-- 1 root root 35G Sep 15 14:37 Prunus-1_1.fastq << MiSeq (500bp).1
-rw-r--r-- 1 root root 35G Sep 15 14:38 Prunus-1_2.fastq << MiSeq (500bp).2
-rw-r--r-- 1 root root 42G Sep 15 14:38 Prunus-2_1.fastq << NextSeq(300bp).1
-rw-r--r-- 1 root root 42G Sep 15 14:40 Prunus-2_2.fastq << NextSeq(300bp).2
MP:
[goonbokim@R820 NextSeq_genome_MP_raw_fastq-gunzip]$ ll -h
total 204G
-rw-r--r-- 1 root root 145K Aug 18 10:12 140814_Prunus_MP_FASTQ.pdf
-rw-r--r-- 1 root root 226 Aug 18 09:57 get_file.md5sum
-rw-r--r-- 1 root root 658 Aug 18 10:12 get_raw_fastq.pl
-rw-r--r-- 1 root root 64 Aug 18 10:12 get_url.txt
-rw------- 1 root root 15M Aug 18 10:12 nohup.out
-rw-r--r-- 1 701 1000 13G Aug 14 15:23 Prun-MP-10kb-1_1.fastq
-rw-r--r-- 1 701 1000 13G Aug 14 15:23 Prun-MP-10kb-1_2.fastq
-rw-r--r-- 1 701 1000 13G Aug 14 15:24 Prun-MP-10kb-2_1.fastq
-rw-r--r-- 1 701 1000 13G Aug 14 15:25 Prun-MP-10kb-2_2.fastq
-rw-r--r-- 1 701 1000 17G Aug 14 15:16 Prun-MP-15kb-1_1.fastq
-rw-r--r-- 1 701 1000 17G Aug 14 15:17 Prun-MP-15kb-1_2.fastq
-rw-r--r-- 1 701 1000 11G Aug 14 15:18 Prun-MP-15kb-2_1.fastq
-rw-r--r-- 1 701 1000 11G Aug 14 15:18 Prun-MP-15kb-2_2.fastq
-rw-r--r-- 1 701 1000 12G Aug 14 15:25 Prun-MP-3kb-1_1.fastq
-rw-r--r-- 1 701 1000 12G Aug 14 15:26 Prun-MP-3kb-1_2.fastq
-rw-r--r-- 1 701 1000 14G Aug 14 15:22 Prun-MP-3kb-2_1.fastq
-rw-r--r-- 1 701 1000 14G Aug 14 15:22 Prun-MP-3kb-2_2.fastq
-rw-r--r-- 1 701 1000 14G Aug 14 15:19 Prun-MP-5kb-1_1.fastq
-rw-r--r-- 1 701 1000 14G Aug 14 15:20 Prun-MP-5kb-1_2.fastq
-rw-r--r-- 1 701 1000 13G Aug 14 15:20 Prun-MP-5kb-2_1.fastq
-rw-r--r-- 1 701 1000 13G Aug 14 15:21 Prun-MP-5kb-2_2.fastq
trimming:
java -jar /Bio/apps/Trimmomatic-0.32/trimmomatic-0.32.jar PE -threads 64 -trimlog ./2.2-trimmomatic/fileindex2.log -phred33 ./raw_split/xaa_1.fastq ./raw_split/xaa_2.fastq ./tr
im_split/xaa_1-p-trim.fastq ./trim_split/xaa_1-u-trim.fastq ./trim_split/xaa_2-p-trim.fastq ./trim_split/xaa_2-u-trim.fastq ILLUMINACLIP:/Bio/apps/Trimmomatic-0.32/adapters/ill
umina-adaptor.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:200
SOAPec
[goonbokim@R820 2.2-trimmomatic]$ ls *.cor.* -lh
-rw-rw-r-- 1 goonbokim goonbokim 31G Nov 13 22:58 Prunus-1_1-paired-trimmed.fastq.cor.pair_1.fq
-rw-rw-r-- 1 goonbokim goonbokim 85 Nov 13 22:58 Prunus-1_1-paired-trimmed.fastq.cor.pair.single.stat
-rw-rw-r-- 1 goonbokim goonbokim 38M Nov 13 22:58 Prunus-1_1-paired-trimmed.fastq.cor.single.fq
-rw-rw-r-- 1 goonbokim goonbokim 719 Nov 13 18:09 Prunus-1_1-paired-trimmed.fastq.cor.stat
-rw-rw-r-- 1 goonbokim goonbokim 2.3G Nov 13 17:39 Prunus-1_1-unpaired-trimmed.fastq.cor.fq
-rw-rw-r-- 1 goonbokim goonbokim 704 Nov 13 17:39 Prunus-1_1-unpaired-trimmed.fastq.cor.stat
-rw-rw-r-- 1 goonbokim goonbokim 28G Nov 13 22:58 Prunus-1_2-paired-trimmed.fastq.cor.pair_2.fq
-rw-rw-r-- 1 goonbokim goonbokim 717 Nov 13 18:45 Prunus-1_2-paired-trimmed.fastq.cor.stat
-rw-rw-r-- 1 goonbokim goonbokim 240M Nov 13 17:40 Prunus-1_2-unpaired-trimmed.fastq.cor.fq
-rw-rw-r-- 1 goonbokim goonbokim 687 Nov 13 17:40 Prunus-1_2-unpaired-trimmed.fastq.cor.stat
-rw-rw-r-- 1 goonbokim goonbokim 39G Nov 13 23:01 Prunus-2_1-paired-trimmed.fastq.cor.pair_1.fq
-rw-rw-r-- 1 goonbokim goonbokim 86 Nov 13 23:01 Prunus-2_1-paired-trimmed.fastq.cor.pair.single.stat
-rw-rw-r-- 1 goonbokim goonbokim 175M Nov 13 23:01 Prunus-2_1-paired-trimmed.fastq.cor.single.fq
-rw-rw-r-- 1 goonbokim goonbokim 723 Nov 13 21:55 Prunus-2_1-paired-trimmed.fastq.cor.stat
-rw-rw-r-- 1 goonbokim goonbokim 2.4G Nov 13 17:46 Prunus-2_1-unpaired-trimmed.fastq.cor.fq
-rw-rw-r-- 1 goonbokim goonbokim 702 Nov 13 17:46 Prunus-2_1-unpaired-trimmed.fastq.cor.stat
-rw-rw-r-- 1 goonbokim goonbokim 38G Nov 13 23:01 Prunus-2_2-paired-trimmed.fastq.cor.pair_2.fq
-rw-rw-r-- 1 goonbokim goonbokim 723 Nov 13 22:37 Prunus-2_2-paired-trimmed.fastq.cor.stat
-rw-rw-r-- 1 goonbokim goonbokim 683M Nov 13 17:47 Prunus-2_2-unpaired-trimmed.fastq.cor.fq
-rw-rw-r-- 1 goonbokim goonbokim 695 Nov 13 17:47 Prunus-2_2-unpaired-trimmed.fastq.cor.stat
MP trimming
nextclip:
[goonbokim@R820 MP]$ nextclip -i /media/NAS/Prunus/NextSeq_genome_MP_raw_fastq-gunzip/Prun-MP-3kb-1_1.fastq -j /media/NAS/Prunus/NextSeq_genome_MP_raw_fastq-gunzip/Prun-MP-3kb-
1_2.fastq -o PyMP3k1 -d
2015년 1월 25일 일요일
2013년 6월 30일 일요일
Ultra Librarian - EAGLE에서 CAD data 사용하기
EAGLE에서 CAD data 사용하기
EAGLE library에 .bxl 형식의 CAD 화일을 추가하는 방법 중에서, Ultra librarian의 사용법을 적어둔다. 먼저 Ultra Librarian을 인스톨한다 (
Ultra Librarian Installer Program for CAD/CAE Schematic Symbols). 설정은 기본으로 두었다.
1. bxl 화일을 EAGLE script로 변환하기
audio selector switch에 사용하려고 TI사의 2채널 DPDT 오디오스위치인 TS5A22364를 선택했다. EAGLE의 기본 라이브러리에는 이 칩의 데이터가 없기 때문에, TI사의 제품 데이터시트에서 (http://www.ti.com/product/ts5a22364#toolssoftware) CAD 데이터를 다운 받는다.
처음 프로그램을 실행하면 이런 폼이 뜨는데, 스텝을 따라가면 된다. Step 1을 눌러서 아까 다운받은 .bxl 파일을 선택한다. Step2는 변환시킬 형식인데 마지막의 Eagle을 선택했다. Step3에서 Export하면 된다.
실행결과가 LOG 창에 뜨는데, 여기에 다음을 위한 절차가 설명되어 있다.
우선 LOG 창의 내용을 보자.
Ultra Librarian Lite 3.0.987 Process Report
Message - Padstack "RX62Y11D0T" Shape(4) is a CIRCLE with no diameter.
Message - Padstack "RX74Y11D0T" Shape(4) is a CIRCLE with no diameter.
Message - Padstack "RX50Y11D0T" Shape(4) is a CIRCLE with no diameter.
TextStyle count: 18
Padstack count: 3
Pattern count: 3
Symbol count: 1
Component count: 1
Export
**********************************************************
************* Important Instructions Follow ************
**********************************************************
All files exported to: C:\UltraLibrarian\Library\Exported\Eagle\2013-07-01_09-29-22.scr
To import your new library into Eagle:
1. Start Eagle.
2. Select File -> New -> Library from the menu.
3. In the blank library window, select File -> Script from the menu.
4. Select the EDIF tab.
5. Browse to the correct Eagle Script file (".scr" file extension) in the file "Open" window.
The exported script file will be below the path configured in Ultra Librarian under
Options -> Configuration -> "Setup" Tab -> "CAD Exports".
6. After opening the file, the script will populate the new library.
7. Use File -> Save (or Save As..) to save the library to the desired location in Eagle native format.
For additional information, please visit this site:
http://www.accelerated-designs.com/help/Eagle_import.html
2. EAGLE library로 저장하기
이제 EAGLE을 실행하고 첫 화면인 Control Panel 윈도우에서, File -> New -> Library를 선택해서 Library 창을 연다.
File -> Execute Script 선택
기본 위치는 C:\UltraLibrarian\Library\Exported\Eagle 인데, 여기서 아까 저장된 최신 파일을 선택한다.
이제, File -> Save As -> Library를 선택해서 부품이름으로 화일을 저장하면 된다.
피드 구독하기:
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