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COMBINE-lab / salmon

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
https://combine-lab.github.io/salmon
GNU General Public License v3.0
779 stars 165 forks source link

Salmon(on galaxy) output only few transcript #824

Open KS751515 opened 1 year ago

KS751515 commented 1 year ago

I am completely new to Bioinfomatic. I started with Galaxy since it require no coding. When execute Salmon, I found the result is very strange.

195 lines format tabular database ?

the length are huge.

Name Length EffectiveLength TPM NumReads 1 248956422 248956245.175 454.257509 2624930.608 10 133797422 133797245.175 273.316948 848802.051 11 135086622 135086445.175 488.035486 1530227.002 12 133275309 133275132.175 506.506671 1566848.399 13 114364328 114364151.175 146.273092 388281.806 14 107043718 107043541.175 349.454058 868246.901 15 101991189 101991012.175 450.603218 1066716.167 16 90338345 90338168.175 396.208587 830783.477 17 83257441 83257264.175 627.875560 1213356.444 18 80373285 80373108.175 134.057567 250089.112 19 58617616 58617439.175 889.185152 1209794.846 2 242193529 242193352.175 386.373763 2172013.559 20 64444167 64443990.175 400.290070 598756.066 21 46709983 46709806.175 321.808746 348898.092 22 50818468 50818291.175 428.166522 505039.621 3 198295559 198295382.175 253.622671 1167329.228 4 190214555 190214378.175 176.536396 779417.738 5 181538259 181538082.175 276.829027 1166465.921 6 170805979 170805802.175 436.693266 1731297.895 7 159345973 159345796.175 293.251440 1084609.614 8 145138636 145138459.175 346.904465 1168651.671 9 138394717 138394540.175 292.533191 939694.730 MT 16569 16392.175 925959.459914 352306.967 X 156040895 156040718.175 182.793129 662049.550 Y 57227415 57227238.175 2.760039 3666.154 KI270728.1 1872759 1872582.175 0.059275 2.576 KI270727.1 448248 448071.175 3.830303 39.836 KI270442.1 392061 391884.175 2.210647 20.108 KI270729.1 280839 280662.175 2.358259 15.363 GL000225.1 211173 210996.175 6.939465 33.985 KI270743.1 210658 210481.175 1.953268 9.543 GL000008.2 209709 209532.175 8.374637 40.730 GL000009.2 201709 201532.175 7.102359 33.223 KI270747.1 198735 198558.175 0.000000 0.000 KI270722.1 194050 193873.175 0.000000 0.000 GL000194.1 191469 191292.175 235.664877 1046.369 KI270742.1 186739 186562.175 16.393393 70.988 GL000205.2 185591 185414.175 75.780709 326.133 GL000195.1 182896 182719.175 121.039913 513.340 KI270736.1 181920 181743.175 0.000000 0.000 KI270733.1 179772 179595.175 30992.190385 129193.190 GL000224.1 179693 179516.175 25.818573 107.579 GL000219.1 179198 179021.175 178.716523 742.612 KI270719.1 176845 176668.175 1.451421 5.952 GL000216.2 176608 176431.175 5.146088 21.074 KI270712.1 176043 175866.175 4.597918 18.769 KI270706.1 175055 174878.175 104.780211 425.312 KI270725.1 172810 172633.175 0.000000 0.000 KI270744.1 168472 168295.175 79.185623 309.322 KI270734.1 165050 164873.175 2.471239 9.457 GL000213.1 164239 164062.175 0.263321 1.003 GL000220.1 161802 161625.175 31217.484649 117111.515 KI270715.1 161471 161294.175 0.000000 0.000 GL000218.1 161147 160970.175 290.561478 1085.616 KI270749.1 158759 158582.175 0.000000 0.000 KI270741.1 157432 157255.175 13.588046 49.597 GL000221.1 155397 155220.175 3.758595 13.541 KI270716.1 153799 153622.175 0.280589 1.000 KI270731.1 150754 150577.175 0.319722 1.117 KI270751.1 150742 150565.175 0.000000 0.000 KI270750.1 148850 148673.175 0.000000 0.000 KI270519.1 138126 137949.175 0.937226 3.001 GL000214.1 137718 137541.175 7.932476 25.324 KI270708.1 127682 127505.175 0.000000 0.000 KI270730.1 112551 112374.175 0.000000 0.000 KI270438.1 112505 112328.175 2.301282 6.000 KI270737.1 103838 103661.175 4.618747 11.113 KI270721.1 100316 100139.175 424.239537 986.070 KI270738.1 99375 99198.175 10.160814 23.395 KI270748.1 93321 93144.175 1.111459 2.403 KI270435.1 92983 92806.175 0.000000 0.000 GL000208.1 92689 92512.175 0.466946 1.003 KI270538.1 91309 91132.175 0.000000 0.000 KI270756.1 79590 79413.175 0.000000 0.000 KI270739.1 73985 73808.175 0.000000 0.000 KI270757.1 71251 71074.175 0.000000 0.000 KI270709.1 66860 66683.175 1.488961 2.305 KI270746.1 66486 66309.175 0.652844 1.005 KI270753.1 62944 62767.175 0.000000 0.000 KI270589.1 44474 44297.175 0.973224 1.001 KI270726.1 43739 43562.175 0.000000 0.000 KI270735.1 42811 42634.175 2.022084 2.001 KI270711.1 42210 42033.175 988.577227 964.485 KI270745.1 41891 41714.175 346.525260 335.514 KI270714.1 41717 41540.175 63.928016 61.639 KI270732.1 41543 41366.175 2.721955 2.613 KI270713.1 40745 40568.175 207.476002 195.365 KI270754.1 40191 40014.175 0.000000 0.000 KI270710.1 40176 39999.175 0.000000 0.000 KI270717.1 40062 39885.175 3.607706 3.340 KI270724.1 39555 39378.175 25.374920 23.193 KI270720.1 39050 38873.175 0.000000 0.000 KI270723.1 38115 37938.175 15.831361 13.941 KI270718.1 38054 37877.175 0.000000 0.000 KI270317.1 37690 37513.175 0.000000 0.000 KI270740.1 37240 37063.175 0.000000 0.000 KI270755.1 36723 36546.175 3.582326 3.039 KI270707.1 32032 31855.175 5.532616 4.091 KI270579.1 31033 30856.175 0.000000 0.000 KI270752.1 27745 27568.175 0.000000 0.000 KI270512.1 22689 22512.175 0.000000 0.000 KI270322.1 21476 21299.175 0.000000 0.000 GL000226.1 15008 14831.175 0.000000 0.000 KI270311.1 12399 12222.175 0.000000 0.000 KI270366.1 8320 8143.175 0.000000 0.000 KI270511.1 8127 7950.175 0.000000 0.000 KI270448.1 7992 7815.175 3.819036 0.693 KI270521.1 7642 7465.175 0.000000 0.000 KI270581.1 7046 6869.175 0.000000 0.000 KI270582.1 6504 6327.175 0.000000 0.000 KI270515.1 6361 6184.175 0.000000 0.000 KI270588.1 6158 5981.175 0.000000 0.000 KI270591.1 5796 5619.175 0.000000 0.000 KI270522.1 5674 5497.175 0.000000 0.000 KI270507.1 5353 5176.175 0.000000 0.000 KI270590.1 4685 4508.175 0.000000 0.000 KI270584.1 4513 4336.175 0.000000 0.000 KI270320.1 4416 4239.175 0.000000 0.000 KI270382.1 4215 4038.175 0.000000 0.000 KI270468.1 4055 3878.175 0.000000 0.000 KI270467.1 3920 3743.175 0.000000 0.000 KI270362.1 3530 3353.175 0.000000 0.000 KI270517.1 3253 3076.175 0.000000 0.000 KI270593.1 3041 2864.175 0.000000 0.000 KI270528.1 2983 2806.175 0.000000 0.000 KI270587.1 2969 2792.175 0.000000 0.000 KI270364.1 2855 2678.175 0.000000 0.000 KI270371.1 2805 2628.175 0.000000 0.000 KI270333.1 2699 2522.175 0.000000 0.000 KI270374.1 2656 2479.175 0.000000 0.000 KI270411.1 2646 2469.175 0.000000 0.000 KI270414.1 2489 2312.175 0.000000 0.000 KI270510.1 2415 2238.175 0.000000 0.000 KI270390.1 2387 2210.175 0.000000 0.000 KI270375.1 2378 2201.175 0.000000 0.000 KI270420.1 2321 2144.175 0.000000 0.000 KI270509.1 2318 2141.175 0.000000 0.000 KI270315.1 2276 2099.175 0.000000 0.000 KI270302.1 2274 2097.175 0.000000 0.000 KI270518.1 2186 2009.175 0.000000 0.000 KI270530.1 2168 1991.175 0.000000 0.000 KI270304.1 2165 1988.175 0.000000 0.000 KI270418.1 2145 1968.175 0.000000 0.000 KI270424.1 2140 1963.175 0.000000 0.000 KI270417.1 2043 1866.175 0.000000 0.000 KI270508.1 1951 1774.175 0.000000 0.000 KI270303.1 1942 1765.175 0.000000 0.000 KI270381.1 1930 1753.175 0.000000 0.000 KI270529.1 1899 1722.175 0.000000 0.000 KI270425.1 1884 1707.175 0.000000 0.000 KI270396.1 1880 1703.175 0.000000 0.000 KI270363.1 1803 1626.175 0.000000 0.000 KI270386.1 1788 1611.175 0.000000 0.000 KI270465.1 1774 1597.175 0.000000 0.000 KI270383.1 1750 1573.175 0.000000 0.000 KI270384.1 1658 1481.175 0.000000 0.000 KI270330.1 1652 1475.175 0.000000 0.000 KI270372.1 1650 1473.175 0.000000 0.000 KI270548.1 1599 1422.175 0.000000 0.000 KI270580.1 1553 1376.175 0.000000 0.000 KI270387.1 1537 1360.175 0.000000 0.000 KI270391.1 1484 1307.175 0.000000 0.000 KI270305.1 1472 1295.175 0.000000 0.000 KI270373.1 1451 1274.175 0.000000 0.000 KI270422.1 1445 1268.175 0.000000 0.000 KI270316.1 1444 1267.175 0.000000 0.000 KI270340.1 1428 1251.175 0.000000 0.000 KI270338.1 1428 1251.175 0.000000 0.000 KI270583.1 1400 1223.175 0.000000 0.000 KI270334.1 1368 1191.175 0.000000 0.000 KI270429.1 1361 1184.175 0.000000 0.000 KI270393.1 1308 1131.175 0.000000 0.000 KI270516.1 1300 1123.175 0.000000 0.000 KI270389.1 1298 1121.175 0.000000 0.000 KI270466.1 1233 1056.175 0.000000 0.000 KI270388.1 1216 1039.175 0.000000 0.000 KI270544.1 1202 1025.175 0.000000 0.000 KI270310.1 1201 1024.175 0.000000 0.000 KI270412.1 1179 1002.175 0.000000 0.000 KI270395.1 1143 966.175 0.000000 0.000 KI270376.1 1136 959.175 0.000000 0.000 KI270337.1 1121 944.175 0.000000 0.000 KI270335.1 1048 871.175 0.000000 0.000 KI270378.1 1048 871.175 0.000000 0.000 KI270379.1 1045 868.175 0.000000 0.000 KI270329.1 1040 863.175 0.000000 0.000 KI270419.1 1029 852.175 0.000000 0.000 KI270336.1 1026 849.175 0.000000 0.000 KI270312.1 998 821.207 0.000000 0.000 KI270539.1 993 816.303 0.000000 0.000 KI270385.1 990 813.358 0.000000 0.000 KI270423.1 981 804.482 0.000000 0.000 KI270392.1 971 794.637 0.000000 0.000 KI270394.1 970 793.658 0.000000 0.000

I use Transcripts FASTA file | 304 : Primary assembly uncompressed

GTF also from ensemble!

the rest I only use default.

Does any body know what could be wrong?

Thank you so much in advance.

KS

rob-p commented 1 year ago

Hi @KS751515,

It appears that you have quantified the genome (i.e. you have computed an abundance for each chromosome) rather than the transcriptome (i.e. an abundance for each gene transcript). The reference should be the reference transcriptome rather than the reference genome (depending on the specific annotation, this should have on the order of ~150,000-200,000 reference sequences.

Best, Rob