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SE51 E. coli ¤³¤ì¤Þ¤Ç¤Î2¥é¥ó¤Î¹ç·× file #¥ê¡¼¥É¿ô ¡ô¥È¥ê¥àºÑ #rrn_map #rrn_unmap %rrn_unmap 5M SE¤Înon-rRNA¤òÆÀ¤ë¤¿¤á¤ËɬÍפÊSE¿ô 5M SE¤Înon-rRNA¤òÆÀ¤ë¤¿¤á¤ËÉÔ¤·¤Æ¤¤¤ëSE¿ô 5M SE¤Înon-rRNA¤òÆÀ¤ë¤¿¤á¤ËɬÍפÊSE¿ô¤ËÂФ¹¤ëͲáÎÌ 181012_10B_S7 17,054,354 17,048,531 15,372,799 1,675,732 9.83 50,886,281 33,831,927 181012_1p2-1_S11 14,637,538 14,632,750 11,399,254 3,233,496 22.09 22,634,229 7,996,691 181012_1p2-2_S13 17,575,234 17,568,939 13,697,563 3,871,376 22.03 22,698,950 5,123,716 181012_2p5-1_S12 11,690,525 11,687,060 8,966,637 2,720,423 23.27 21,486,594 9,796,069 181012_2p6-1_S14 16,662,621 16,657,233 12,576,242 4,080,991 24.49 20,414,920 3,752,299 181012_45a_plus_S2 18,990,853 18,985,343 14,055,624 4,929,719 25.96 19,261,598 270,745 181012_45b_plus_S3 15,055,824 15,052,797 11,717,495 3,335,302 22.15 22,570,406 7,514,582 181012_45c_plus_S4 21,339,929 21,336,596 16,477,436 4,859,160 22.77 21,958,455 618,526 181013_45A_minus_S18 16,532,044 16,524,826 6,155,460 10,369,366 62.72 7,971,579 *** 8,560,465 181019_43B_S1 14,923,538 14,920,375 10,969,417 3,950,958 26.47 18,885,974 3,962,436 181019_45A_plus_S5 16,869,266 16,865,671 12,115,849 4,749,822 28.16 17,757,788 888,522 181019_45L_S6 12,808,719 12,805,744 8,250,496 4,555,248 35.56 14,059,299 1,250,580 181019_45a10D_plus_S9 16,210,966 16,205,968 13,420,227 2,785,741 17.18 29,096,327 12,885,361 181019_45aIII6c_plus_S8 15,696,596 15,690,006 12,927,019 2,762,987 17.60 28,405,121 12,708,525 181019_45d7B_plus_S10 13,268,830 13,264,315 11,154,294 2,110,021 15.90 31,442,412 18,173,582 181026_10D_minus_S21 20,353,513 20,344,812 10,544,708 9,800,104 48.15 10,384,335 *** 9,969,178 181026_2-10B_minus_S20 20,487,318 20,476,914 9,177,453 11,299,461 55.15 9,065,617 *** 11,421,701 181026_45a_minus_S15 17,516,312 17,510,720 9,034,910 8,475,810 48.39 10,333,120 *** 7,183,192 181026_45b_minus_S16 15,943,050 15,937,770 7,184,469 8,753,301 54.90 9,106,879 *** 6,836,171 181026_45c_minus_S17 14,383,563 14,376,676 5,640,314 8,736,362 60.74 8,232,010 *** 6,151,553 181103_45alll6c_minus_S22 21,788,554 21,781,657 10,052,049 11,729,608 53.83 9,287,844 *** 12,500,710 181103_45d7B_minus_S23 22,149,677 22,140,700 16,750,927 5,389,773 24.33 20,547,876 *** 1,601,801 181103_Anc_S19 17,975,953 17,964,999 13,759,979 4,205,020 23.39 21,374,397 3,398,444 PwOw_minus_S25 18,853,776 18,849,002 8,300,103 10,548,899 55.95 8,936,371 *** 9,917,405 PwOw_plus_S24 19,269,944 19,263,287 14,659,892 4,603,395 23.89 20,930,144 1,660,200 123,832,204
16S, 23S, 5S
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¥Ç¡¼¥¿¥Ù¡¼¥¹¤Ï¡©¡¡¡¡¥Ç¥£¥ì¥¯¥È¥ê ~/src/sortmerna-2.1b/rRNA_databases¤ò³Îǧ silva-arc-16s-id95.fasta arcaea ¸ÅºÙ¶Ý silva-arc-23s-id98.fasta silva-bac-16s-id90.fasta bacterium ºÙ¶Ý silva-bac-23s-id98.fasta silva-euk-18s-id95.fasta eukaryota ¿¿³ËÀ¸Êª silva-euk-28s-id98.fasta rfam-5s-database-id98.fasta rfam-5.8s-database-id98.fasta
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cd ~/src/sortmerna-2.1b indexdb_rna --ref ./rRNA_databases/silva-bac-16s-id90.fasta,./index/silva-bac-16s-db:\ ./rRNA_databases/silva-bac-23s-id98.fasta,./index/silva-bac-23s-db:\ ./rRNA_databases/silva-arc-16s-id95.fasta,./index/silva-arc-16s-db:\ ./rRNA_databases/silva-arc-23s-id98.fasta,./index/silva-arc-23s-db:\ ./rRNA_databases/silva-euk-18s-id95.fasta,./index/silva-euk-18s-db:\ ./rRNA_databases/silva-euk-28s-id98.fasta,./index/silva-euk-28s:\ ./rRNA_databases/rfam-5s-database-id98.fasta,./index/rfam-5s-db:\ ./rRNA_databases/rfam-5.8s-database-id98.fasta,./index/rfam-5.8s-db
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/src/KishimotoRNA2/181012_10B_S7_R1_001.trim.fastq ¤ò»î¤·¤Æ¤ß¤ë¡£
sortmerna --ref ./rRNA_databases/silva-bac-16s-id90.fasta,./index/silva-bac-16s-db:\ ./rRNA_databases/silva-bac-23s-id98.fasta,./index/silva-bac-23s-db:\ ./rRNA_databases/rfam-5s-database-id98.fasta,./index/rfam-5s-db:\ ./rRNA_databases/rfam-5.8s-database-id98.fasta,./index/rfam-5.8s-db \ --reads 181012_10B_S7_R1_001.trim.fastq --sam --num_alignments 1 --fastx --aligned 181012_10B_S7_R1_001.rRNA \ --other 181012_10B_S7_R1_001.trim.non_rRNA --log -v
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Program: SortMeRNA version 2.1b, 03/03/2016 Copyright: 2012-16 Bonsai Bioinformatics Research Group: LIFL, University Lille 1, CNRS UMR 8022, INRIA Nord-Europe 2014-16 Knight Lab: Department of Pediatrics, UCSD, La Jolla, Disclaimer: SortMeRNA comes with ABSOLUTELY NO WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. Contact: Evguenia Kopylova, jenya.kopylov@gmail.com Laurent Noé, laurent.noe@lifl.fr Hélène Touzet, helene.touzet@lifl.fr Computing read file statistics ... done [23.20 sec] size of reads file: 2906733904 bytes partial section(s) to be executed: 3 of size 1073741824 bytes Parameters summary: Number of seeds = 2 Edges = 4 (as integer) SW match = 2 SW mismatch = -3 SW gap open penalty = 5 SW gap extend penalty = 2 SW ambiguous nucleotide = -3 SQ tags are not output Number of threads = 1 Begin mmap reads section # 1: Time to mmap reads and set up pointers [1.37 sec] Begin analysis of: ./rRNA_databases/silva-bac-16s-id90.fasta Seed length = 18 Pass 1 = 18, Pass 2 = 9, Pass 3 = 3 Gumbel lambda = 0.602725 Gumbel K = 0.329559 Minimal SW score based on E-value = 59 Loading index part 1/1 ... done [1.34 sec] Begin index search ... done [719.52 sec] Freeing index ... done [0.24 sec] Begin analysis of: ./rRNA_databases/silva-bac-23s-id98.fasta Seed length = 18 Pass 1 = 18, Pass 2 = 9, Pass 3 = 3 Gumbel lambda = 0.602436 Gumbel K = 0.335011 Minimal SW score based on E-value = 58 Loading index part 1/1 ... done [1.00 sec] Begin index search ... done [1471.22 sec] Freeing index ... done [0.16 sec] Begin analysis of: ./rRNA_databases/rfam-5s-database-id98.fasta Seed length = 18 Pass 1 = 18, Pass 2 = 9, Pass 3 = 3 Gumbel lambda = 0.616694 Gumbel K = 0.342032 Minimal SW score based on E-value = 56 Loading index part 1/1 ... done [0.60 sec] Begin index search ... done [143.74 sec] Freeing index ... done [0.08 sec] Begin analysis of: ./rRNA_databases/rfam-5.8s-database-id98.fasta Seed length = 18 Pass 1 = 18, Pass 2 = 9, Pass 3 = 3 Gumbel lambda = 0.617555 Gumbel K = 0.343861 Minimal SW score based on E-value = 54 Loading index part 1/1 ... done [0.22 sec] Begin index search ... done [111.06 sec] Freeing index ... done [0.03 sec] Total number of reads mapped (incl. all reads file sections searched): 5800992 Writing aligned FASTA/FASTQ ... done [18.38 sec] Writing not-aligned FASTA/FASTQ ... done [1.82 sec] Begin mmap reads section # 2: Time to mmap reads and set up pointers [1.53 sec] Begin analysis of: ./rRNA_databases/silva-bac-16s-id90.fasta Loading index part 1/1 ... done [1.44 sec] Begin index search ... done [690.19 sec] Freeing index ... done [0.27 sec] Begin analysis of: ./rRNA_databases/silva-bac-23s-id98.fasta Loading index part 1/1 ... done [0.93 sec] Begin index search ... done [1429.56 sec] Freeing index ... done [0.14 sec] Begin analysis of: ./rRNA_databases/rfam-5s-database-id98.fasta Loading index part 1/1 ... done [0.58 sec] Begin index search ... done [140.79 sec] Freeing index ... done [0.07 sec] Begin analysis of: ./rRNA_databases/rfam-5.8s-database-id98.fasta Loading index part 1/1 ... done [0.21 sec] Begin index search ... done [111.21 sec] Freeing index ... done [0.02 sec] Total number of reads mapped (incl. all reads file sections searched): 11563780 Writing aligned FASTA/FASTQ ... done [19.83 sec] Writing not-aligned FASTA/FASTQ ... done [2.13 sec] Begin mmap reads section # 3: Time to mmap reads and set up pointers [1.07 sec] Begin analysis of: ./rRNA_databases/silva-bac-16s-id90.fasta Loading index part 1/1 ... done [1.42 sec] Begin index search ... done [523.39 sec] Freeing index ... done [0.26 sec] Begin analysis of: ./rRNA_databases/silva-bac-23s-id98.fasta Loading index part 1/1 ... done [0.93 sec] Begin index search ... done [1039.06 sec] Freeing index ... done [0.18 sec] Begin analysis of: ./rRNA_databases/rfam-5s-database-id98.fasta Loading index part 1/1 ... done [0.60 sec] Begin index search ... done [100.63 sec] Freeing index ... done [0.07 sec] Begin analysis of: ./rRNA_databases/rfam-5.8s-database-id98.fasta Loading index part 1/1 ... done [0.22 sec] Begin index search ... done [80.05 sec] Freeing index ... done [0.02 sec] Total number of reads mapped (incl. all reads file sections searched): 15633981 Writing aligned FASTA/FASTQ ... done [13.92 sec] Writing not-aligned FASTA/FASTQ ... done [1.40 sec]
¥í¥°¥Õ¥¡¥¤¥ë 181012_10B_S7_R1_001.rRNA.log
Tue Jul 23 16:59:31 2019 Command: sortmerna --ref ./rRNA_databases/silva-bac-16s-id90.fasta,./index/silva-bac-16s-db:./rRNA_databases/silva-bac-23s-id98.fasta,./index/silva-bac-23s-db:./rRNA_databases/rfam-5s-database-id98.fasta,./index/rfam-5s-db:./rRNA_databases/rfam-5.8s-database-id98.fasta,./index/rfam-5.8s-db --reads 181012_10B_S7_R1_001.trim.fastq --sam --num_alignments 1 --fastx --aligned 181012_10B_S7_R1_001.rRNA --other 181012_10B_S7_R1_001.trim.non_rRNA.fastq fastq -v Process pid = 70967 Parameters summary: Index: ./index/silva-bac-16s-db Seed length = 18 Pass 1 = 18, Pass 2 = 9, Pass 3 = 3 Gumbel lambda = 0.602725 Gumbel K = 0.329559 Minimal SW score based on E-value = 59 Index: ./index/silva-bac-23s-db Seed length = 18 Pass 1 = 18, Pass 2 = 9, Pass 3 = 3 Gumbel lambda = 0.602436 Gumbel K = 0.335011 Minimal SW score based on E-value = 58 Index: ./index/rfam-5s-db Seed length = 18 Pass 1 = 18, Pass 2 = 9, Pass 3 = 3 Gumbel lambda = 0.616694 Gumbel K = 0.342032 Minimal SW score based on E-value = 56 Index: ./index/rfam-5.8s-db Seed length = 18 Pass 1 = 18, Pass 2 = 9, Pass 3 = 3 Gumbel lambda = 0.617555 Gumbel K = 0.343861 Minimal SW score based on E-value = 54 Number of seeds = 2 Edges = 4 (as integer) SW match = 2 SW mismatch = -3 SW gap open penalty = 5 SW gap extend penalty = 2 SW ambiguous nucleotide = -3 SQ tags are not output Number of threads = 1 Reads file = 181012_10B_S7_R1_001.trim.fastq Results: Total reads = 17049704 Total reads passing E-value threshold = 15633981 (91.70%) Total reads failing E-value threshold = 1415723 (8.30%) Minimum read length = 36 Maximum read length = 51 Mean read length = 50 By database: ./rRNA_databases/silva-bac-16s-id90.fasta 20.37% ./rRNA_databases/silva-bac-23s-id98.fasta 71.31% ./rRNA_databases/rfam-5s-database-id98.fasta 0.02% ./rRNA_databases/rfam-5.8s-database-id98.fasta 0.00% Tue Jul 23 18:50:05 2019
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wc -l 181012_10B_S7_R1_001.fastq 68217416 181012_10B_S7_R1_001.fastq¡¡¡¡4¤Ç³ä¤ë¤È 17,054,354
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wc -l 181012_10B_S7_R1_001.trim.fastq 68198816 181012_10B_S7_R1_001.trim.fastq¡¡¡¡4¤Ç³ä¤ë¤È 17,049,704
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wc -l 181012_10B_S7_R1_001.rRNA.fastq¡¡¤Ç¬Äê 62,535,924 181012_10B_S7_R1_001.rRNA.fastq¡¡¡¡4¤Ç³ä¤ë¤È 15,633,981 5,662,892 181012_10B_S7_R1_001.trim.non_rRNA.fastq¡¡4¤Ç³ä¤ë¤È 1,415,723
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡Â¤¹¤È 17,049,704
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file #¥ê¡¼¥É¿ô ¡ô¥È¥ê¥àºÑ #rrn_map #rrn_unmap %rrn_unmap 181012_10B_S7 17,054,354 17,048,531 15,372,799 1,675,732 9.83
ʬΥ¸åÆÀ¤é¤ì¤¿r-RNA¤Îsam¥Õ¥¡¥¤¥ë¡¡181012_10B_S7_R1_001.rRNA.sam ¤ÎÀèÆ¬¤ò¼è¤ê½Ð¤·¤ÆÇÁ¤¤¤Æ¤ß¤ë¡£
head -500 181012_10B_S7_R1_001.rRNA.sam > 181012_10B_S7_R1_001.rRNA-500.sam
@HD VN:1.0 SO:unsorted @PG ID:sortmerna VN:1.0 CL:sortmerna --ref ./rRNA_databases/silva-bac-16s-id90.fasta,./index/silva-bac-16s-db:./rRNA_databases/silva-bac-23s-id98.fasta,./index/silva-bac-23s-db:./rRNA_databases/rfam-5s-database-id98.fasta,./index/rfam-5s-db:./rRNA_databases/rfam-5.8s-database-id98.fasta,./index/rfam-5.8s-db --reads 181012_10B_S7_R1_001.trim.fastq --sam --num_alignments 1 --fastx --aligned 181012_10B_S7_R1_001.rRNA --other 181012_10B_S7_R1_001.trim.non_rRNA.fastq fastq -v C00122:247:HLWJLBCX2:1:1101:10535:2128 0 FU8Pinit 117 255 1S47M3S * 0 0 TATTGCTAGCGATTCCGACTTCATGGAGTCGAGTTGCAGACTCCAATCCGG DDDDDIIIIIIIIIIIIIIIIIIIIIIIIGIIIIIIIIIIIIIIIIHIIII AS:i:79 NM:i:3 C00122:247:HLWJLBCX2:1:1101:12824:2040 0 FU8Pinit 121 255 49M2S * 0 0 CTAGCGATTCCGACTTCATGGAGTCGAGTTGCAGACTCCAATCCGGACTAC DDDDDIIIIGIIHIIIIIIIHIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:78 NM:i:4 C00122:247:HLWJLBCX2:1:1101:10750:2503 0 FU8Pinit 123 255 47M4S * 0 0 AGCGATTCCGACTTCATGGAGTCGAGTTGCAGACTCCAATCCGGACTACGA DDDDDHHIIHIIHIIIIIIIIIIIIIIIIIGIHIIHIIHIIIIGIIIIIID AS:i:74 NM:i:4 C00122:247:HLWJLBCX2:1:1101:8130:2894 0 Unc13453 1436 255 5S3M1D43M * 0 0 CCTACGGTTACCTTGTTTCGACTTCACCCCAGTCATGAATCACAAAGTGGT DDDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:82 NM:i:2 C00122:247:HLWJLBCX2:1:1101:19062:2832 0 FU8Pinit 70 255 36M1D15M * 0 0 GTGTACAAGGCCCGGGAACGTATTCACCGTGGCATTCTGACCCACGATTAC DDDDDIIIIIIIIIIIIIIIIIIIIIHIIIIIIIIIIIIIIHIIIIHIIII AS:i:62 NM:i:8 C00122:247:HLWJLBCX2:1:1101:6236:3120 0 FU8Pinit 134 255 4S36M11S * 0 0 CCGACTTCATGGAGTCGAGTTGCAGACTCCAATCCGGACTACGACGCACTT DDDDDHIIIIIIGHIIIIIIHIIHIHIIIIIIIIIIHGHHIHIIIIIIIII AS:i:62 NM:i:2 C00122:247:HLWJLBCX2:1:1101:3119:3328 0 FU8Pinit 81 255 25M1D25M1S * 0 0 CCGGGAACGTATTCACCGTGGCATTCTGATCCACGATTACTAGCGATTCCG DDDDDIHIIIIHIIIIIIIIIIIIIIIHIIIIIIIHIIIIIIHIIIIIIIH AS:i:75 NM:i:5 C00122:247:HLWJLBCX2:1:1101:6916:3312 0 FU8Pinit 75 255 1S31M1D19M * 0 0 ACAAGGCCCGGGAACGTATTCACCGTGGCATTCTGATCCACGATTACTAGC DDDDDIIIIIGHHDHIHIIIIIIIIIIHIGIIIIIIIIIIIIIHIHIHIII AS:i:70 NM:i:6 C00122:247:HLWJLBCX2:1:1101:14490:3742 0 Unc13453 1436 255 6S3M1D42M * 0 0 CCCTACGGTTACCTTGTTCCGACTTCACCCCAGTCATGAATCACAAAGTGG DDDDDHHGHHHIIIHHIIGHIIIHHGIHIHIFHHHHHH?FHHEHHGHHIII AS:i:80 NM:i:2 C00122:247:HLWJLBCX2:1:1101:10644:3794 0 FU8Pinit 75 255 31M1D20M * 0 0 CAAGGCCCGGGAACGTATTCACCGTGGCATTCTGATCCACGATTACTAGCG DDDDDHIIIIIHIIIIIHHIIIIIIIIIHIIIIIIIIIIIIIIIHIIIHII AS:i:72 NM:i:6 C00122:247:HLWJLBCX2:1:1101:12145:3862 0 FU8Pinit 51 255 49M2S * 0 0 CCGTGGTGTGACGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCGTGG DDDDDIIIIIIIIIHHIIIIIIIIIIIIHIIIIIIIIIIIIIIIHIIIIII AS:i:73 NM:i:5 C00122:247:HLWJLBCX2:1:1101:14381:3795 0 FU8Pinit 124 255 46M5S * 0 0 GCGATTCCGACTTCATGGAGTCGAGTTGCAGACTCCAATCCGGACTACGAC DDDDDIIIIGHIIIHEHHIGHIIIGIIIIIIIIHHHIIIIIIDIIIIIIII AS:i:72 NM:i:4 C00122:247:HLWJLBCX2:1:1101:20932:3891 0 Unc13453 1436 255 5S3M1D43M * 0 0 CCTACGGTTACCTTGTTCCGACTTCACCCCAGTCATGAATCACAAAGTGGT DDDDDHHIIIIIHHIHIIHIIIIIIIIIHHIHFHHHHIIHGIHIIIIIIII AS:i:82 NM:i:2 C00122:247:HLWJLBCX2:1:1101:20311:4173 0 FU8Pinit 59 255 1S47M1D3M * 0 0 GTGACGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCGTGGCATTCTG <D@DBCHIDHI<CEHIIHEGHIIHIIIGHHIDHH?EHHIGHIFHII?FHGH AS:i:75 NM:i:5 C00122:247:HLWJLBCX2:1:1101:9967:4272 0 I6CCervi 5 255 1S43M7S * 0 0 CCGACTTGCATGTGTTAGGCCTGCCGCCAGCGTTCAATCTGAGCCATGATC DDDDDIIHIHIIHHIIIIHIIIIIIIIIIIIIHIIIIIIIIHIIIIIIIII AS:i:86 NM:i:0 C00122:247:HLWJLBCX2:1:1101:5980:4705 0 FU8Pinit 52 255 48M3S * 0 0 CATGGTGTGACGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCGTGGC DDDDDIIIIHHIIIIIIIIIIIIIIIIHHIIIIIIIIIIIIIIIIIIIIII AS:i:76 NM:i:4 C00122:247:HLWJLBCX2:1:1101:7670:4720 0 FU8Pinit 123 255 47M4S * 0 0 AGCGATTCCGACTTCATGGAGTCGAGTTGCAGACTCCAATCCGGACTACGA DDDDDIIIIIHIIIIIIIHIIIIIIIIIIIIIIIIIIIIIIIIIIIHIIII AS:i:74 NM:i:4 C00122:247:HLWJLBCX2:1:1101:14848:4727 0 Unc13453 1436 255 1S3M1D47M * 0 0 CGGTTACCTTGTTACGACTTCACCCCAGTCATGAATCACAAAGTGGTAAGC DDDDDIIIIIIIIIIIIIIIHIIIH<EH<GHHIGIIIIIIIIIIHIIIIII AS:i:90 NM:i:2
non-rRNA¤Îfastq¥Õ¥¡¥¤¥ë¤ò¡¢¥Þ¥Ã¥Ô¥ó¥°¤·¤Æ¡¢¤É¤ì¤À¤±Æó½Å¥Þ¥Ã¥×¤¬¤¢¤ë¤«½Ð¤·¤Æ¤ß¤ë¡£
nohup hisat2 -p 16 --dta-cufflinks -x AP012030.fna -U 181012_10B_S7_R1_001.trim.non_rRNA.fastq -S 181012_10B_S7_R1_001.trim.non_rRNA.sam > 181012_10B_S7_R1_001.trim.non_rRNA.hisat2.log &
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1415723 reads; of these: 1415723 (100.00%) were unpaired; of these: 30855 (2.18%) aligned 0 times 1366651 (96.53%) aligned exactly 1 time 18217 (1.29%) aligned >1 times 97.82% overall alignment rate
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