Problem with Mageck paired analysis

Question

[toma.85]

Dear all, I have a matter to submit. I'm trying to do a paired analysis, however, I'm getting this error. Error: incorrect number of dimensions in line 2 (16) compared with the header line (4). Please double-check your read count table file. This is the header of my count matrix and it doesn't seem to have apparently problem

$ head COUNTS_paired_sor_T0.count.txt
sgRNA Gene SOR_r1 SOR_r1 SOR_r1 SOR_r2 SOR_r2 SOR_r2 SOR_r2 T0_r1 T0_r1 T0_r1 T0_r2 T0_r2 T0_r2 T0_r2 T0_r2 T0_r2
Pgd_sg155_1 Pgd 2989 995 1685 908 1127 1264 1196 1110 666 413 959 1391 1357 1235 1375 1366
Smn1_sg208_4 Smn1 4792 1854 2605 1333 1772 2158 2242 2046 1201 710 1577 2433 2574 2037 2010 2033
Cyp27a1_sg044_3 Cyp27a1 3210 1307 1746 885 713 562 642 660 671 362 819 1281 770 647 616 673
Gca_sg079_3 Gca 4815 1544 2527 1571 869 810 866 880 860 533 1240 1895 1218 748 1046 831
Gstk1_sg087_5 Gstk1 2998 1130 1819 1037 2214 2459 2508 2431 849 443 1029 1724 3030 2230 2501 2508
Ddo_sg048_3 Ddo 2765 1176 1780 911 863 787 885 884 628 313 793 1511 1250 834 910 894
Ehhadh_sg057_3 Ehhadh 5063 1674 3002 1512 2347 2594 2740 2944 1091 680 1533 3007 2856 2361 2621 2293
Mapk1_sg117_2 Mapk1 5369 2006 3483 1893 877 1216 934 1069 1273 709 1522 2837 1654 1260 1305 1267
Rbm6_sg183_6 Rbm6 7618 2926 4661 2568 2136 2332 2215 2283 1434 790 1914 3226 2617 2044 2337 2007

the commands I used are the following:

mageck test -k COUNTS_paired_sor_T0.count.txt -t SOR_r1 SOR_r1 SOR_r1 SOR_r1 SOR_r2 SOR_r2 SOR_r2 SOR_r2 -c T0_r1 T0_r1 T0_r1 T0_r1 T0_r2 T0_r2 T0_r2 T0_r2 -n sor_T0_paired --paired

Can anyone suggest a solution? thank you

[GenoMax]

As noted in MAGeCK wiki you need to use the names or indexes as a comma separated list. Are those 4 replicates per condition?If you may want to call them SOR_r1_1 SOR_r1_2 etc.

Then do

mageck test -k COUNTS_paired_sor_T0.count.txt -t SOR_r1_1,SOR_r1_2,... 

[Meisam]

Yes, @toma.85 you have to provide "unique" labels for each replicate in your count file, otherwise MAGeCK does not know which sample you are referring to even if you want them as replicates, as GenoMax pointed out above. See this part from the wiki: https://sourceforge.net/p/mageck/wiki/QA/#how-to-perform-paired-analysis