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Make a ribosomal RNA interval_list for Picard Tools CollectRnaSeqMetrics
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| @SQ SN:chrM LN:16571 | |
| @SQ SN:chr1 LN:249250621 | |
| @SQ SN:chr2 LN:243199373 | |
| @SQ SN:chr3 LN:198022430 | |
| @SQ SN:chr4 LN:191154276 | |
| @SQ SN:chr5 LN:180915260 | |
| @SQ SN:chr6 LN:171115067 | |
| @SQ SN:chr7 LN:159138663 | |
| @SQ SN:chr8 LN:146364022 | |
| @SQ SN:chr9 LN:141213431 | |
| @SQ SN:chr10 LN:135534747 | |
| @SQ SN:chr11 LN:135006516 | |
| @SQ SN:chr12 LN:133851895 | |
| @SQ SN:chr13 LN:115169878 | |
| @SQ SN:chr14 LN:107349540 | |
| @SQ SN:chr15 LN:102531392 | |
| @SQ SN:chr16 LN:90354753 | |
| @SQ SN:chr17 LN:81195210 | |
| @SQ SN:chr18 LN:78077248 | |
| @SQ SN:chr19 LN:59128983 | |
| @SQ SN:chr20 LN:63025520 | |
| @SQ SN:chr21 LN:48129895 | |
| @SQ SN:chr22 LN:51304566 | |
| @SQ SN:chrX LN:155270560 | |
| @SQ SN:chrY LN:59373566 | |
| chr1 9497728 9497837 - ENST00000517147.1 | |
| chr1 13949679 13949779 - ENST00000411020.1 | |
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| chr4 8394742 8394851 + ENST00000365184.1 | |
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| chr11 124506355 124506488 + ENST00000363408.1 | |
| chr12 13593818 13593935 - ENST00000364606.1 | |
| chr12 26526531 26526666 - ENST00000391247.1 | |
| chr12 28658327 28658461 + ENST00000365317.1 | |
| chr12 30459364 30459457 - ENST00000515972.1 | |
| chr12 34358634 34358752 + ENST00000607318.1 | |
| chr12 38555268 38555384 - ENST00000362973.1 | |
| chr12 38557205 38557317 - ENST00000364838.1 | |
| chr12 42052478 42052595 + ENST00000516555.1 | |
| chr12 45511554 45511671 + ENST00000362686.1 | |
| chr12 66460001 66460118 + ENST00000516048.1 | |
| chr12 80272085 80272199 - ENST00000365072.1 | |
| chr12 88445478 88445555 + ENST00000516938.1 | |
| chr12 90120713 90120819 + ENST00000516398.1 | |
| chr12 99477561 99477683 - ENST00000365454.1 | |
| chr12 101866117 101866234 + ENST00000516557.1 | |
| chr12 102173592 102173707 + ENST00000364298.1 | |
| chr12 102230598 102230705 + ENST00000411114.1 | |
| chr12 104519014 104519134 + ENST00000362545.1 | |
| chr12 107880288 107880412 - ENST00000410370.1 | |
| chr12 109497791 109497905 + ENST00000390836.1 | |
| chr12 111777331 111777425 + ENST00000517271.1 | |
| chr12 119267486 119267610 + ENST00000362939.1 | |
| chr12 123767463 123767581 - ENST00000362975.1 | |
| chr12 131784185 131784296 - ENST00000390949.1 | |
| chr12 132145608 132145719 + ENST00000390852.1 | |
| chr12 132285860 132285979 - ENST00000363646.1 | |
| chr12 133300531 133300643 - ENST00000364599.1 | |
| chr13 19662627 19662721 + ENST00000516478.1 | |
| chr13 21943929 21944038 - ENST00000410815.1 | |
| chr13 38428989 38429107 - ENST00000362406.1 | |
| chr13 46125620 46125738 - ENST00000363839.1 | |
| chr13 51387124 51387242 - ENST00000363841.1 | |
| chr13 51601883 51601988 - ENST00000410988.1 | |
| chr13 58565484 58565598 + ENST00000365552.1 | |
| chr13 61187742 61187868 + ENST00000411144.1 | |
| chr13 72552226 72552344 + ENST00000363167.1 | |
| chr13 79963669 79963766 - ENST00000516687.1 | |
| chr13 90787966 90788095 - ENST00000516887.1 | |
| chr13 94677724 94677852 - ENST00000391257.1 | |
| chr13 95303651 95303783 - ENST00000410197.1 | |
| chr13 98015226 98015355 - ENST00000365420.1 | |
| chr13 106807721 106807839 - ENST00000410750.1 | |
| chr13 108953560 108953679 - ENST00000411245.1 | |
| chr14 20558289 20558386 + ENST00000517190.1 | |
| chr14 20614276 20614314 - ENST00000516076.1 | |
| chr14 20883146 20883257 + ENST00000363355.1 | |
| chr14 24627812 24627931 + ENST00000362934.1 | |
| chr14 50019351 50019466 + ENST00000516615.1 | |
| chr14 52159470 52159579 + ENST00000515947.1 | |
| chr14 68123822 68123928 - ENST00000607639.1 | |
| chr14 76070516 76070621 + ENST00000364226.1 | |
| chr14 78644146 78644264 - ENST00000362584.1 | |
| chr14 107092677 107092791 + ENST00000362610.1 | |
| chr15 25983655 25983767 + ENST00000410191.1 | |
| chr15 27525465 27525583 - ENST00000363456.1 | |
| chr15 40623738 40623849 - ENST00000516905.1 | |
| chr15 42144111 42144227 - ENST00000363423.1 | |
| chr15 50274640 50274758 + ENST00000364216.1 | |
| chr15 50755578 50755695 + ENST00000516567.1 | |
| chr15 59866302 59866421 - ENST00000364834.1 | |
| chr15 61028968 61029085 + ENST00000391323.1 | |
| chr15 69659924 69660020 + ENST00000517163.1 | |
| chr15 72150911 72151027 + ENST00000364003.1 | |
| chr15 86681500 86681610 - ENST00000517155.1 | |
| chr15 98015356 98015482 - ENST00000515920.1 | |
| chr15 100614286 100614395 - ENST00000517148.1 | |
| chr16 9658247 9658354 - ENST00000363598.1 | |
| chr16 9693954 9694085 + ENST00000517118.1 | |
| chr16 26040233 26040346 + ENST00000363059.1 | |
| chr16 33965426 33965577 + ENST00000363564.1 | |
| chr16 34968764 34968875 + ENST00000516106.1 | |
| chr16 34969010 34969119 + ENST00000410275.1 | |
| chr16 34969743 34969842 + ENST00000516115.1 | |
| chr16 34969996 34970104 + ENST00000516815.1 | |
| chr16 34980360 34980465 + ENST00000516285.1 | |
| chr16 34981403 34981511 + ENST00000516373.1 | |
| chr16 34984432 34984546 + ENST00000517246.1 | |
| chr16 34985945 34986055 + ENST00000516838.1 | |
| chr16 34986199 34986306 + ENST00000516459.1 | |
| chr16 34987197 34987313 + ENST00000515951.1 | |
| chr16 34988167 34988301 + ENST00000515908.1 | |
| chr16 34988417 34988553 + ENST00000516997.1 | |
| chr16 34988926 34989059 + ENST00000516864.1 | |
| chr16 34989294 34989404 + ENST00000516778.1 | |
| chr16 34989548 34989656 + ENST00000517127.1 | |
| chr16 47484258 47484372 - ENST00000390988.1 | |
| chr16 47539343 47539454 + ENST00000410336.1 | |
| chr16 50903366 50903486 - ENST00000362901.1 | |
| chr16 53371365 53371483 + ENST00000365323.1 | |
| chr16 66335712 66335843 + ENST00000365129.1 | |
| chr16 68776383 68776491 + ENST00000363688.1 | |
| chr16 75894946 75895055 - ENST00000362429.1 | |
| chr16 79298351 79298470 + ENST00000410312.1 | |
| chr16 84073523 84073638 - ENST00000362480.1 | |
| chr16 84296421 84296534 - ENST00000364491.1 | |
| chr17 3960050 3960170 - ENST00000516647.1 | |
| chr17 6504264 6504371 - ENST00000364044.1 | |
| chr17 15685655 15685769 + ENST00000516020.1 | |
| chr17 30290824 30290952 - ENST00000517249.1 | |
| chr17 32447075 32447186 - ENST00000516561.1 | |
| chr17 34847043 34847166 - ENST00000517103.1 | |
| chr17 36888055 36888173 - ENST00000363245.1 | |
| chr17 38530341 38530428 + ENST00000516809.1 | |
| chr17 39874406 39874512 + ENST00000365050.1 | |
| chr17 43404732 43404863 - ENST00000363083.1 | |
| chr17 64263861 64263966 + ENST00000516844.1 | |
| chr17 64635387 64635501 + ENST00000515889.1 | |
| chr17 64891608 64891689 + ENST00000515955.1 | |
| chr17 65264226 65264344 + ENST00000363749.1 | |
| chr17 72413733 72413843 - ENST00000363151.1 | |
| chr18 9844714 9844843 - ENST00000516871.1 | |
| chr18 9923917 9924018 + ENST00000411206.1 | |
| chr18 19508946 19509055 - ENST00000410588.1 | |
| chr18 21750469 21750587 - ENST00000363004.1 | |
| chr18 29756013 29756131 - ENST00000362503.1 | |
| chr18 39850554 39850680 + ENST00000517231.1 | |
| chr18 41651548 41651666 + ENST00000365190.1 | |
| chr18 46001858 46001971 - ENST00000364002.1 | |
| chr18 47472636 47472759 - ENST00000363657.1 | |
| chr18 47845372 47845490 + ENST00000516188.1 | |
| chr18 52813777 52813876 - ENST00000516628.1 | |
| chr18 70419187 70419286 + ENST00000516789.1 | |
| chr18 75575420 75575523 - ENST00000516451.1 | |
| chr19 453134 453245 + ENST00000516730.1 | |
| chr19 7951862 7951981 - ENST00000363030.1 | |
| chr19 12107624 12107731 + ENST00000516251.1 | |
| chr19 12138728 12138836 - ENST00000391195.1 | |
| chr19 12180979 12181086 + ENST00000516737.1 | |
| chr19 12217312 12217429 + ENST00000391274.1 | |
| chr19 18082834 18082926 + ENST00000516782.1 | |
| chr19 21295934 21296042 - ENST00000364165.1 | |
| chr19 24187160 24187309 - ENST00000365096.1 | |
| chr19 29492577 29492682 + ENST00000516463.1 | |
| chr19 32146262 32146367 - ENST00000516971.1 | |
| chr19 32734871 32734989 - ENST00000363868.1 | |
| chr19 58874805 58874929 + ENST00000516402.1 | |
| chr20 5079033 5079122 - ENST00000391234.1 | |
| chr20 5326652 5326806 - ENST00000363443.1 | |
| chr20 15261410 15261519 - ENST00000410568.1 | |
| chr20 18414486 18414588 + ENST00000516613.1 | |
| chr20 21119597 21119715 - ENST00000362639.1 | |
| chr20 23141494 23141608 - ENST00000364657.1 | |
| chr20 23361533 23361649 - ENST00000364858.1 | |
| chr20 29944673 29944781 + ENST00000516840.1 | |
| chr20 30596154 30596275 + ENST00000516814.1 | |
| chr20 30638391 30638508 + ENST00000391269.1 | |
| chr20 33783109 33783226 + ENST00000363431.1 | |
| chr20 39482759 39482869 - ENST00000458857.1 | |
| chr20 44188397 44188515 - ENST00000365053.1 | |
| chr20 46501935 46502017 + ENST00000515961.1 | |
| chr20 54780108 54780229 - ENST00000410186.1 | |
| chr21 15443192 15443307 + ENST00000364942.1 | |
| chr21 26574521 26574629 + ENST00000410986.2 | |
| chr21 33935385 33935520 + ENST00000517141.1 | |
| chr21 38224211 38224328 + ENST00000362936.1 | |
| chr21 43641283 43641396 + ENST00000411330.1 | |
| chr22 22146723 22146813 + ENST00000364115.1 | |
| chr22 26111008 26111136 - ENST00000410653.1 | |
| chr22 26786633 26786742 - ENST00000516458.1 | |
| chr22 31701390 31701498 + ENST00000391240.1 | |
| chr22 33031088 33031184 - ENST00000516081.1 | |
| chrX 1419149 1419268 - ENST00000411342.1 | |
| chrX 9101869 9101987 + ENST00000363982.1 | |
| chrX 29000969 29001087 - ENST00000364486.1 | |
| chrX 32120182 32120293 + ENST00000410990.1 | |
| chrX 41152051 41152169 + ENST00000362694.1 | |
| chrX 48065693 48065809 + ENST00000517047.1 | |
| chrX 52694281 52694397 + ENST00000410676.1 | |
| chrX 53935488 53935595 + ENST00000364748.1 | |
| chrX 68892323 68892441 + ENST00000606950.1 | |
| chrX 69472892 69473012 + ENST00000363603.1 | |
| chrX 75875410 75875528 - ENST00000411327.1 | |
| chrX 76287130 76287248 + ENST00000364577.1 | |
| chrX 94837063 94837161 + ENST00000364697.1 | |
| chrX 103105726 103105840 - ENST00000410487.1 | |
| chrX 110913057 110913176 - ENST00000364550.1 | |
| chrX 128570507 128570624 - ENST00000364648.1 | |
| chrX 131072874 131072984 - ENST00000363717.1 | |
| chrX 134562093 134562210 - ENST00000364570.1 | |
| chrX 141498839 141498957 + ENST00000364130.1 | |
| chrX 145508974 145509090 - ENST00000364724.1 | |
| chrX 147089620 147089735 - ENST00000364415.1 | |
| chrX 150194767 150194878 - ENST00000391293.1 | |
| chrY 1369149 1369268 - ENSTR0000411342.1 | |
| chrY 9928019 9928137 - ENST00000515957.1 | |
| chrY 9930484 9930602 - ENST00000516480.1 | |
| chrY 10037764 10037915 + ENST00000515896.1 | |
| chrY 19669744 19669856 + ENST00000516506.1 | |
| chrY 19671654 19671769 + ENST00000516203.1 | |
| chrY 20508009 20508124 - ENST00000516144.1 | |
| chrY 20509921 20510033 - ENST00000516858.1 |
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| #!/usr/bin/env bash | |
| # make_rRNA.sh | |
| # Kamil Slowikowski | |
| # December 12, 2014 | |
| # Modified by António Domingues to include other species | |
| # and rRNA in Bed format | |
| ########################## | |
| ## Usage | |
| ########################## | |
| usage() { | |
| echo " Usage: `basename $0` genomeVersion rRNA.bed" | |
| echo " Creates a rRNA interval list suitable for RNASEQ-QC" | |
| echo "" | |
| echo "example: `basename $0` hg19 rRNA.[bed/GTF]" | |
| echo "" | |
| echo " The expected inputs are:" | |
| echo " arg1=genomic locations of rRNAs either in bed format, or a Gencode GTF" | |
| echo " Gencode files can be obtained from (hg19) ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_19/gencode.v19.annotation.gtf.gz" | |
| echo " Look for the chromosome sizes file in the current folder, e.g. hg19.chrom.sizes. If not present it will download the information from UCSC." | |
| exit 2 | |
| } | |
| ## if less than three arguments supplied, display usage | |
| if [ $# -le 1 ] | |
| then | |
| usage | |
| exit 1 | |
| fi | |
| ## set the input variables | |
| export genome=$1 | |
| rRNA_file=$2 | |
| chrom_sizes=$genome.chrom.sizes | |
| # 1. Download Chromosome sizes from the UCSC genome browser | |
| if [[ ! -s $chrom_sizes ]] | |
| then | |
| echo "File with chromosome sizes was not found." | |
| echo "Downloading from UCSC..." | |
| mysql -N --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \ | |
| "SELECT chrom,size FROM chromInfo ORDER BY size DESC;" $genome \ | |
| > $chrom_sizes | |
| echo "Done." | |
| fi | |
| # 2. rRNA interval_list file | |
| ## is it a bed file or a GTF? | |
| filename=$(basename "$rRNA_file") | |
| extension="${filename##*.}" | |
| echo $extension | |
| if [[ $extension == "bed" ]] | |
| then | |
| echo "rRNA is in $extension format" | |
| # Output file suitable for Picard tools | |
| rRNA=$genome.rRNA.interval_list | |
| # Sequence names and lengths. (Must be tab-delimited.) | |
| perl -lane 'print "\@SQ\tSN:$F[0]\tLN:$F[1]\tAS:$ENV{'genome'}"' $chrom_sizes | \ | |
| grep -v _ \ | |
| >> $rRNA | |
| # Intervals for rRNA transcripts. | |
| cat $rRNA_file | \ | |
| awk -v OFS='\t' '{print $1, $2, $3, $6, $4}' | \ | |
| sort -k1V -k2n -k3n \ | |
| >> $rRNA | |
| echo "rRNA interval file created. Have fun." | |
| elif [[ $extension == "gtf" ]] | |
| then | |
| echo "rRNA is in $extension format" | |
| # Output file suitable for Picard tools | |
| rRNA=$genome.rRNA.interval_list | |
| # Sequence names and lengths. (Must be tab-delimited.) | |
| perl -lane 'print "\@SQ\tSN:$F[0]\tLN:$F[1]\tAS:$ENV{'genome'}"' $chrom_sizes | \ | |
| grep -v _ \ | |
| >> $rRNA | |
| # Intervals for rRNA transcripts. | |
| grep 'gene_type "rRNA"' $rRNA_file | \ | |
| awk '$3 == "transcript"' | \ | |
| cut -f1,4,5,7,9 | \ | |
| perl -lane ' | |
| /transcript_id "([^"]+)"/ or die "no transcript_id on $."; | |
| print join "\t", (@F[0,1,2,3], $1) | |
| ' | \ | |
| sort -k1V -k2n -k3n \ | |
| >> $rRNA | |
| echo "rRNA interval file created. Have fun." | |
| else | |
| echo "Please make sure that the file format with the rNA locations is either bed or gtf, and the extension match 'bed' or 'gtf'." | |
| fi |
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Now includes other species and include other species and rRNA in Bed format.