Hi,
I have a file like this:
[chr10 165453 165506 NB551726:5:H2HT5BGXC:2:21303:24622:7645 1 -
chr10 166943 166996 NB551726:5:H2HT5BGXC:1:21204:26106:6737 0 -
chr10 190746 190799 NB551726:5:H2HT5BGXC:4:21407:6393:8844 0 -
chr10 198550 198601 NB551726:5:H2HT5BGXC:2:12103:20108:8195 0 -]
and I am using grep -v to remove both 0 and 1 at the same time, but it is not working.
apmcd47
September 12, 2019, 3:52pm
2
Please give an example of what your output should look like. Because the file as listed has 0s and 1s on all lines, and therefore grep as you propose to use it will delete all lines,
Andrew
1 Like
chr10 85261 85334 NB551726:5:H2HT5BGXC:1:12302:10118:15866 1 +
chr10 86743 86797 NB551726:5:H2HT5BGXC:4:23505:9965:12318 1 -
chr10 152763 152818 NB551726:5:H2HT5BGXC:1:11101:11832:4136 21 +
chr10 165453 165506 NB551726:5:H2HT5BGXC:2:21303:24622:7645 1 -
chr10 166943 166996 NB551726:5:H2HT5BGXC:1:21204:26106:6737 0 -
chr10 190746 190799 NB551726:5:H2HT5BGXC:4:21407:6393:8844 0 -
chr10 198550 198601 NB551726:5:H2HT5BGXC:2:12103:20108:8195 0 -
chr10 198859 198912 NB551726:5:H2HT5BGXC:2:23106:23104:16217 1 -
chr10 253095 253145 NB551726:5:H2HT5BGXC:1:12208:13468:12307 1 -
chr10 253673 253726 NB551726:5:H2HT5BGXC:1:21105:3541:19675 1 +
chr10 270718 270779 NB551726:5:H2HT5BGXC:1:21302:6151:20084 36 +
chr10 279976 280049 NB551726:5:H2HT5BGXC:2:13202:7290:18772 42 +
chr10 283222 283281 NB551726:5:H2HT5BGXC:1:11101:10679:13185 22 +
chr10 295639 295667 NB551726:5:H2HT5BGXC:2:23312:6151:17914 22 +
chr10 299560 299613 NB551726:5:H2HT5BGXC:1:23201:2570:5802 36 +
chr10 305259 305319 NB551726:5:H2HT5BGXC:1:11108:11822:9076 36 +
chr10 312027 312074 NB551726:5:H2HT5BGXC:2:12205:3503:10905 1 +
chr10 326693 326754 NB551726:5:H2HT5BGXC:3:12409:12174:3620 36 +
chr10 333356 333417 NB551726:5:H2HT5BGXC:3:11612:14865:1631 36 +
chr10 342529 342583 NB551726:5:H2HT5BGXC:1:11103:5762:7412 1 +
chr10 379970 380025 NB551726:5:H2HT5BGXC:2:23309:24673:10995 1 -
chr10 390585 390649 NB551726:5:H2HT5BGXC:2:21201:17184:1970 41 -
chr10 403073 403135 NB551726:5:H2HT5BGXC:4:22411:12518:10842 36 +
chr10 434880 434942 NB551726:5:H2HT5BGXC:1:11104:1268:15557 21 +
chr10 483038 483100 NB551726:5:H2HT5BGXC:2:22311:25390:20113 11 +
chr10 503546 503580 NB551726:5:H2HT5BGXC:4:13503:22757:1800 22 +
chr10 508971 509024 NB551726:5:H2HT5BGXC:2:21311:2213:13019 1 +
chr10 523026 523082 NB551726:5:H2HT5BGXC:3:12610:14716:4694 44 -
chr10 556875 556935 NB551726:5:H2HT5BGXC:3:11402:15158:12217 36 +
chr10 572659 572731 NB551726:5:H2HT5BGXC:3:23406:8429:3838 42 +
chr10 632605 632666 NB551726:5:H2HT5BGXC:4:21501:15836:16570 36 +
chr10 654420 654525 NB551726:5:H2HT5BGXC:3:11511:18064:17880 0 -
chr10 695526 695596 NB551726:5:H2HT5BGXC:1:13301:7447:12370 42 -
chr10 703974 704036 NB551726:5:H2HT5BGXC:2:11306:16949:4387 12 -
chr10 745719 745782 NB551726:5:H2HT5BGXC:4:22510:13285:17813 41 +
chr10 777527 777553 NB551726:5:H2HT5BGXC:1:12206:12418:9864 0 +
and the output should have all the other entries except the lines having 0 and 1 in the 5th column.
RudiC
September 12, 2019, 4:20pm
4
Try
grep -v " [01] *[+-]" file
2 Likes
gull04
September 13, 2019, 3:25am
6
Hi,
Can you post the output to show how it doesn't work, that would be more helpfull.
Regards
Gull04
2 Likes
RudiC
September 13, 2019, 4:29am
7
Does:
grep -v " [01] *[+-]" file
chr10 152763 152818 NB551726:5:H2HT5BGXC:1:11101:11832:4136 21 +
chr10 270718 270779 NB551726:5:H2HT5BGXC:1:21302:6151:20084 36 +
chr10 279976 280049 NB551726:5:H2HT5BGXC:2:13202:7290:18772 42 +
chr10 283222 283281 NB551726:5:H2HT5BGXC:1:11101:10679:13185 22 +
chr10 295639 295667 NB551726:5:H2HT5BGXC:2:23312:6151:17914 22 +
chr10 299560 299613 NB551726:5:H2HT5BGXC:1:23201:2570:5802 36 +
chr10 305259 305319 NB551726:5:H2HT5BGXC:1:11108:11822:9076 36 +
chr10 326693 326754 NB551726:5:H2HT5BGXC:3:12409:12174:3620 36 +
chr10 333356 333417 NB551726:5:H2HT5BGXC:3:11612:14865:1631 36 +
chr10 390585 390649 NB551726:5:H2HT5BGXC:2:21201:17184:1970 41 -
chr10 403073 403135 NB551726:5:H2HT5BGXC:4:22411:12518:10842 36 +
chr10 434880 434942 NB551726:5:H2HT5BGXC:1:11104:1268:15557 21 +
chr10 483038 483100 NB551726:5:H2HT5BGXC:2:22311:25390:20113 11 +
chr10 503546 503580 NB551726:5:H2HT5BGXC:4:13503:22757:1800 22 +
chr10 523026 523082 NB551726:5:H2HT5BGXC:3:12610:14716:4694 44 -
chr10 556875 556935 NB551726:5:H2HT5BGXC:3:11402:15158:12217 36 +
chr10 572659 572731 NB551726:5:H2HT5BGXC:3:23406:8429:3838 42 +
chr10 632605 632666 NB551726:5:H2HT5BGXC:4:21501:15836:16570 36 +
chr10 695526 695596 NB551726:5:H2HT5BGXC:1:13301:7447:12370 42 -
chr10 703974 704036 NB551726:5:H2HT5BGXC:2:11306:16949:4387 12 -
chr10 745719 745782 NB551726:5:H2HT5BGXC:4:22510:13285:17813 41 +
2 Likes
chr10 83450 83503 NB551726:5:H2HT5BGXC:1:23210:11622:11362 1 +
chr10 83673 83765 NB551726:5:H2HT5BGXC:2:21205:17604:2246 0 +
chr10 85504 85558 NB551726:5:H2HT5BGXC:2:22211:7601:16419 31 +
chr10 85636 85689 NB551726:5:H2HT5BGXC:3:13612:11620:17539 1 -
chr10 86068 86121 NB551726:5:H2HT5BGXC:4:12406:24783:2749 1 -
chr10 87062 87115 NB551726:5:H2HT5BGXC:1:11304:16254:3825 1 +
chr10 90463 90516 NB551726:5:H2HT5BGXC:1:11102:24833:4879 1 +
chr10 99875 99929 NB551726:5:H2HT5BGXC:1:12201:7805:1705 0 +
chr10 106760 106813 NB551726:5:H2HT5BGXC:3:12506:12571:10460 1 -
chr10 146518 146570 NB551726:5:H2HT5BGXC:1:22112:11102:14366 14 -
chr10 164895 164940 NB551726:5:H2HT5BGXC:1:13211:15930:15082 1 -
chr10 166771 166824 NB551726:5:H2HT5BGXC:1:12101:20188:17034 1 +
chr10 198434 198467 NB551726:5:H2HT5BGXC:1:11306:7431:3548 0 -
chr10 232590 232630 NB551726:5:H2HT5BGXC:1:12308:2911:4998 18 +
chr10 233673 233721 NB551726:5:H2HT5BGXC:1:11204:24661:6499 24 +
chr10 244426 244461 NB551726:5:H2HT5BGXC:4:22610:1450:10242 22 -
chr10 283223 283277 NB551726:5:H2HT5BGXC:1:21202:24027:11672 44 +
chr10 287019 287063 NB551726:5:H2HT5BGXC:1:22210:5587:11665 28 +
chr10 336049 336112 NB551726:5:H2HT5BGXC:4:21402:23402:10596 36 -
chr10 342089 342142 NB551726:5:H2HT5BGXC:1:13310:11131:11654 1 -
chr10 342529 342583 NB551726:5:H2HT5BGXC:1:11211:9508:1997 1 +
chr10 362697 362752 NB551726:5:H2HT5BGXC:1:11101:11174:14176 42 -
chr10 371287 371340 NB551726:5:H2HT5BGXC:4:11602:10047:13747 44 +
chr10 388618 388671 NB551726:5:H2HT5BGXC:1:11306:6809:18821 24 +
chr10 420131 420159 NB551726:5:H2HT5BGXC:2:23203:13675:14982 22 -
chr10 476607 476640 NB551726:5:H2HT5BGXC:3:22501:13073:17530 22 -
chr10 500144 500198 NB551726:5:H2HT5BGXC:2:11301:24584:1760 44 +
chr10 509180 509213 NB551726:5:H2HT5BGXC:1:11106:7603:13116 0 +
chr10 511342 511395 NB551726:5:H2HT5BGXC:1:23110:18078:12881 1 +
chr10 585380 585424 NB551726:5:H2HT5BGXC:2:12304:5393:1266 9 +
chr10 685059 685121 NB551726:5:H2HT5BGXC:1:21101:21058:3630 11 +
chr10 685205 685266 NB551726:5:H2HT5BGXC:3:11408:1925:8674 1 +
chr10 685352 685413 NB551726:5:H2HT5BGXC:3:23408:13668:1449 0 +
chr10 731130 731159 NB551726:5:H2HT5BGXC:1:13202:15125:10876 0 +
chr10 794077 794130 NB551726:5:H2HT5BGXC:1:11306:15879:10062 1 -
chr10 794971 795024 NB551726:5:H2HT5BGXC:3:21404:4215:19571 1 +
chr10 795264 795317 NB551726:5:H2HT5BGXC:2:13206:6134:9929 1 +
chr10 795524 795560 NB551726:5:H2HT5BGXC:2:21205:15853:5080 0 -
chr10 814780 814815 NB551726:5:H2HT5BGXC:4:13412:1664:12073 22 +
chr10 837668 837722 NB551726:5:H2HT5BGXC:1:11101:25458:6217 44 +
chr10 947014 947075 NB551726:5:H2HT5BGXC:2:12102:8014:4477 17 -
chr10 973816 973878 NB551726:5:H2HT5BGXC:1:11101:10787:4355 22 +
chr10 1012283 1012336 NB551726:5:H2HT5BGXC:1:23308:13195:10976 1 +
chr10 1026458 1026492 NB551726:5:H2HT5BGXC:3:11506:7661:3547 0 -
chr10 1037982 1038035 NB551726:5:H2HT5BGXC:3:13608:13694:9588 44 -
chr10 1046219 1046262 NB551726:5:H2HT5BGXC:1:21202:3219:4865 2 -
chr10 1064331 1064378 NB551726:5:H2HT5BGXC:3:23406:24220:15886 0 -
chr10 1104334 1104387 NB551726:5:H2HT5BGXC:1:12103:16042:13671 44 +
chr10 1195895 1195988 NB551726:5:H2HT5BGXC:1:11106:13477:18629 24 +
chr10 1267381 1267426 NB551726:5:H2HT5BGXC:1:11104:13034:2182 1 -
chr10 1271055 1271108 NB551726:5:H2HT5BGXC:1:21209:2410:17494 1 +
chr10 1287684 1287737 NB551726:5:H2HT5BGXC:1:21211:11389:17162 1 +
chr10 1301770 1301823 NB551726:5:H2HT5BGXC:1:22211:19077:10160 1 +
chr10 1302816 1302869 NB551726:5:H2HT5BGXC:1:13101:17304:13773 1 +
chr10 1305284 1305341 NB551726:5:H2HT5BGXC:3:12601:23177:5879 1 +
chr10 1346480 1346533 NB551726:5:H2HT5BGXC:3:11408:4043:10920 1 -
chr10 1347666 1347719 NB551726:5:H2HT5BGXC:2:23210:23276:18735 1 +
chr10 1349156 1349209 NB551726:5:H2HT5BGXC:4:12506:4480:3779 1 -
chr10 1349869 1349922 NB551726:5:H2HT5BGXC:2:12109:10808:14290 1 -
chr10 1367503 1367553 NB551726:5:H2HT5BGXC:4:22610:5848:13809 24 +
chr10 1431352 1431392 NB551726:5:H2HT5BGXC:4:13601:10331:9778 9 +
chr10 1494893 1494940 NB551726:5:H2HT5BGXC:3:21601:4179:7024 1 +
chr10 1494948 1494990 NB551726:5:H2HT5BGXC:1:11103:26564:4480 1 -
chr10 1504933 1504976 NB551726:5:H2HT5BGXC:3:11506:21284:7335 0 -
chr10 1513840 1513893 NB551726:5:H2HT5BGXC:2:21101:1240:14937 1 -
chr10 1526949 1527003 NB551726:5:H2HT5BGXC:1:11106:4035:1555 44 +
chr10 1535924 1535977 NB551726:5:H2HT5BGXC:1:11109:6188:7918 1 -
chr10 1549714 1549765 NB551726:5:H2HT5BGXC:1:11205:14522:3538 44 +
chr10 1579039 1579093 NB551726:5:H2HT5BGXC:4:12407:2657:10053 1 +
chr10 1580121 1580165 NB551726:5:H2HT5BGXC:1:21206:18826:14008 11 +
chr10 1606485 1606538 NB551726:5:H2HT5BGXC:1:22112:9279:5865 1 +
chr10 1606828 1606881 NB551726:5:H2HT5BGXC:3:22408:20983:8297 1 +
chr10 1811297 1811350 NB551726:5:H2HT5BGXC:2:11110:2868:16729 1 -
chr10 1812327 1812380 NB551726:5:H2HT5BGXC:3:22512:22115:5787 1 +
chr10 1825561 1825590 NB551726:5:H2HT5BGXC:1:11110:2129:4021 0 -
chr10 1842110 1842171 NB551726:5:H2HT5BGXC:2:11310:26839:10836 28 +
chr10 1881715 1881753 NB551726:5:H2HT5BGXC:2:11205:3952:19358 2 +
chr10 1922335 1922390 NB551726:5:H2HT5BGXC:3:11602:6835:13982 44 +
chr10 1991697 1991766 NB551726:5:H2HT5BGXC:1:13212:5870:20182 36 +
chr10 2101162 2101215 NB551726:5:H2HT5BGXC:1:21107:12547:7522 44 +
chr10 2244348 2244386 NB551726:5:H2HT5BGXC:2:11108:18028:9665 0 +
chr10 2292698 2292726 NB551726:5:H2HT5BGXC:3:13403:8382:4801 22 -
chr10 2296869 2296922 NB551726:5:H2HT5BGXC:2:13301:11582:18251 1 -
chr10 2366208 2366259 NB551726:5:H2HT5BGXC:1:12212:14624:16575 40 +
chr10 2396479 2396509 NB551726:5:H2HT5BGXC:3:22509:15130:13568 9 +
chr10 2396527 2396581 NB551726:5:H2HT5BGXC:2:22301:3292:6255 2 +
chr10 2518990 2519044 NB551726:5:H2HT5BGXC:1:11109:9354:2230 41 -
chr10 2533231 2533269 NB551726:5:H2HT5BGXC:4:11406:26398:8923 0 -
chr10 2534234 2534287 NB551726:5:H2HT5BGXC:4:22410:16649:7949 1 -
chr10 2534702 2534755 NB551726:5:H2HT5BGXC:3:13405:17174:6905 1 -
chr10 2570819 2570875 NB551726:5:H2HT5BGXC:1:11101:17058:14296 22 -
chr10 2598458 2598510 NB551726:5:H2HT5BGXC:4:23402:11741:2459 9 -
chr10 2645231 2645267 NB551726:5:H2HT5BGXC:4:23407:13046:7808 22 -
chr10 2664360 2664405 NB551726:5:H2HT5BGXC:1:12212:2600:16692 2 -
chr10 2689748 2689785 NB551726:5:H2HT5BGXC:2:13101:24861:12307 22 -
chr10 2757729 2757782 NB551726:5:H2HT5BGXC:2:13110:17135:7589 44 +
chr10 2767042 2767088 NB551726:5:H2HT5BGXC:1:22107:4789:12466 2 +
chr10 2803427 2803454 NB551726:5:H2HT5BGXC:2:11203:24404:19669 22 -
chr10 2814113 2814167 NB551726:5:H2HT5BGXC:1:12305:14313:9805 44 -
chr10 2932828 2932881 NB551726:5:H2HT5BGXC:2:11301:21719:1970 1 +
chr10 3034873 3034907 NB551726:5:H2HT5BGXC:1:23109:21910:9724 2 +
chr10 3124175 3124207 NB551726:5:H2HT5BGXC:1:22111:5657:13463 0 +
chr10 3420171 3420224 NB551726:5:H2HT5BGXC:1:12210:2214:14077 41 -
chr10 3420565 3420622 NB551726:5:H2HT5BGXC:1:11104:13745:15948 36 +
chr10 3534307 3534340 NB551726:5:H2HT5BGXC:1:13203:20883:2767 0 +
chr10 3606289 3606342 NB551726:5:H2HT5BGXC:2:11112:20795:16887 44 -
chr10 3618574 3618610 NB551726:5:H2HT5BGXC:1:13207:15169:14738 24 -
chr10 3621035 3621064 NB551726:5:H2HT5BGXC:2:11307:6461:10417 22 -
chr10 3646540 3646586 NB551726:5:H2HT5BGXC:2:22110:5058:7733 11 +
chr10 3647767 3647804 NB551726:5:H2HT5BGXC:1:11101:24494:6143 22 +
chr10 3681373 3681414 NB551726:5:H2HT5BGXC:3:21404:25227:19317 2 -
chr10 3683054 3683110 NB551726:5:H2HT5BGXC:1:11107:12183:9835 19 +
chr10 3687341 3687385 NB551726:5:H2HT5BGXC:3:22603:1787:10818 9 -
chr10 3723453 3723491 NB551726:5:H2HT5BGXC:2:22106:13995:13538 0 +
chr10 3731481 3731507 NB551726:5:H2HT5BGXC:4:13407:26161:10111 22 +
chr10 3773260 3773316 NB551726:5:H2HT5BGXC:1:11101:8820:18166 22 +
gull04
September 13, 2019, 8:05am
9
Hi,
Using the data that you provided in the previous post and the "grep" already supplied I get;
[e434069@fbakirpomd4 data]$ grep -v " [01] *[+-]" test_01.txt
chr10 85504 85558 NB551726:5:H2HT5BGXC:2:22211:7601:16419 31 +
chr10 146518 146570 NB551726:5:H2HT5BGXC:1:22112:11102:14366 14 -
chr10 232590 232630 NB551726:5:H2HT5BGXC:1:12308:2911:4998 18 +
chr10 233673 233721 NB551726:5:H2HT5BGXC:1:11204:24661:6499 24 +
chr10 244426 244461 NB551726:5:H2HT5BGXC:4:22610:1450:10242 22 -
chr10 283223 283277 NB551726:5:H2HT5BGXC:1:21202:24027:11672 44 +
chr10 287019 287063 NB551726:5:H2HT5BGXC:1:22210:5587:11665 28 +
chr10 336049 336112 NB551726:5:H2HT5BGXC:4:21402:23402:10596 36 -
chr10 362697 362752 NB551726:5:H2HT5BGXC:1:11101:11174:14176 42 -
chr10 371287 371340 NB551726:5:H2HT5BGXC:4:11602:10047:13747 44 +
chr10 388618 388671 NB551726:5:H2HT5BGXC:1:11306:6809:18821 24 +
chr10 420131 420159 NB551726:5:H2HT5BGXC:2:23203:13675:14982 22 -
chr10 476607 476640 NB551726:5:H2HT5BGXC:3:22501:13073:17530 22 -
chr10 500144 500198 NB551726:5:H2HT5BGXC:2:11301:24584:1760 44 +
chr10 585380 585424 NB551726:5:H2HT5BGXC:2:12304:5393:1266 9 +
chr10 685059 685121 NB551726:5:H2HT5BGXC:1:21101:21058:3630 11 +
chr10 814780 814815 NB551726:5:H2HT5BGXC:4:13412:1664:12073 22 +
chr10 837668 837722 NB551726:5:H2HT5BGXC:1:11101:25458:6217 44 +
chr10 947014 947075 NB551726:5:H2HT5BGXC:2:12102:8014:4477 17 -
chr10 973816 973878 NB551726:5:H2HT5BGXC:1:11101:10787:4355 22 +
chr10 1037982 1038035 NB551726:5:H2HT5BGXC:3:13608:13694:9588 44 -
chr10 1046219 1046262 NB551726:5:H2HT5BGXC:1:21202:3219:4865 2 -
chr10 1104334 1104387 NB551726:5:H2HT5BGXC:1:12103:16042:13671 44 +
chr10 1195895 1195988 NB551726:5:H2HT5BGXC:1:11106:13477:18629 24 +
chr10 1367503 1367553 NB551726:5:H2HT5BGXC:4:22610:5848:13809 24 +
chr10 1431352 1431392 NB551726:5:H2HT5BGXC:4:13601:10331:9778 9 +
chr10 1526949 1527003 NB551726:5:H2HT5BGXC:1:11106:4035:1555 44 +
chr10 1549714 1549765 NB551726:5:H2HT5BGXC:1:11205:14522:3538 44 +
chr10 1580121 1580165 NB551726:5:H2HT5BGXC:1:21206:18826:14008 11 +
chr10 1842110 1842171 NB551726:5:H2HT5BGXC:2:11310:26839:10836 28 +
chr10 1881715 1881753 NB551726:5:H2HT5BGXC:2:11205:3952:19358 2 +
chr10 1922335 1922390 NB551726:5:H2HT5BGXC:3:11602:6835:13982 44 +
chr10 1991697 1991766 NB551726:5:H2HT5BGXC:1:13212:5870:20182 36 +
chr10 2101162 2101215 NB551726:5:H2HT5BGXC:1:21107:12547:7522 44 +
chr10 2292698 2292726 NB551726:5:H2HT5BGXC:3:13403:8382:4801 22 -
chr10 2366208 2366259 NB551726:5:H2HT5BGXC:1:12212:14624:16575 40 +
chr10 2396479 2396509 NB551726:5:H2HT5BGXC:3:22509:15130:13568 9 +
chr10 2396527 2396581 NB551726:5:H2HT5BGXC:2:22301:3292:6255 2 +
chr10 2518990 2519044 NB551726:5:H2HT5BGXC:1:11109:9354:2230 41 -
chr10 2570819 2570875 NB551726:5:H2HT5BGXC:1:11101:17058:14296 22 -
chr10 2598458 2598510 NB551726:5:H2HT5BGXC:4:23402:11741:2459 9 -
chr10 2645231 2645267 NB551726:5:H2HT5BGXC:4:23407:13046:7808 22 -
chr10 2664360 2664405 NB551726:5:H2HT5BGXC:1:12212:2600:16692 2 -
chr10 2689748 2689785 NB551726:5:H2HT5BGXC:2:13101:24861:12307 22 -
chr10 2757729 2757782 NB551726:5:H2HT5BGXC:2:13110:17135:7589 44 +
chr10 2767042 2767088 NB551726:5:H2HT5BGXC:1:22107:4789:12466 2 +
chr10 2803427 2803454 NB551726:5:H2HT5BGXC:2:11203:24404:19669 22 -
chr10 2814113 2814167 NB551726:5:H2HT5BGXC:1:12305:14313:9805 44 -
chr10 3034873 3034907 NB551726:5:H2HT5BGXC:1:23109:21910:9724 2 +
chr10 3420171 3420224 NB551726:5:H2HT5BGXC:1:12210:2214:14077 41 -
chr10 3420565 3420622 NB551726:5:H2HT5BGXC:1:11104:13745:15948 36 +
chr10 3606289 3606342 NB551726:5:H2HT5BGXC:2:11112:20795:16887 44 -
chr10 3618574 3618610 NB551726:5:H2HT5BGXC:1:13207:15169:14738 24 -
chr10 3621035 3621064 NB551726:5:H2HT5BGXC:2:11307:6461:10417 22 -
chr10 3646540 3646586 NB551726:5:H2HT5BGXC:2:22110:5058:7733 11 +
chr10 3647767 3647804 NB551726:5:H2HT5BGXC:1:11101:24494:6143 22 +
chr10 3681373 3681414 NB551726:5:H2HT5BGXC:3:21404:25227:19317 2 -
chr10 3683054 3683110 NB551726:5:H2HT5BGXC:1:11107:12183:9835 19 +
chr10 3687341 3687385 NB551726:5:H2HT5BGXC:3:22603:1787:10818 9 -
chr10 3731481 3731507 NB551726:5:H2HT5BGXC:4:13407:26161:10111 22 +
chr10 3773260 3773316 NB551726:5:H2HT5BGXC:1:11101:8820:18166 22 +
Which looks to be correct.
Regards
Gull04
2 Likes
Perhaps tab characters were converted to spaces? Often copy/paste of text does it.
The awk sample in the previous post works with tabs or spaces.
Hey Amit,
grep doesn't really work on delimited row data, rather it works as individual character in the file.
in your case awk is always a better approach. You may try the below: (assuming you are using tab delimiter from your example)
awk -F "\t" '($5) > 1' filename | sort -u | cut -d '\t' -f 1,2,3,4,5,6 > outputfile
Thanks!
1 Like
system
May 7, 2020, 12:47pm
13
Moderator comments were removed during original forum migration.
Neo
May 7, 2020, 12:59pm
14
@Amit_Pande
Did you solve this?
If so, please post your solution back so the community can benefit.
Thanks.
Neo
June 6, 2020, 12:59pm
15
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