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
