I am trying to use grep to pull out express values.
I run eXpress and I have my .xprs tab separated value file which looks like this:
bundle_id target_id length eff_length tot_counts uniq_counts est_counts eff_counts ambig_distr_alpha ambig_distr_beta fpkm fpkm_conf_low fpkm_conf_high solvable
1 Contig14365 310 106.787904 85 85 85.000000 246.750792 0.000000e+00 0.000000e+00 147.370523 147.370523 147.370523 T
2 Singlet_45262 346 232.432874 109 37 89.933541 133.875234 1.998601e+00 7.198885e-01 71.637085 51.273440 92.000730 T
2 Singlet_68764 236 119.092916 74 2 21.066459 41.746263 6.254955e+00 1.736541e+01 32.750608 0.142967 65.358248 T
3 Contig1270 736 500.694431 50 0 0.125252 0.184116 1.000000e+00 1.000000e+00 0.046316 0.000000 0.759071 F
3 Contig1271 851 628.717767 57 9 43.657462 59.092492 4.701649e-01 1.810055e-01 12.856315 4.051524 21.661106 T
3 Singlet_69558 790 555.880836 50 0 15.217286 21.626318 1.000000e+00 1.000000e+00 5.068381 0.000000 12.670313 F
I want to get non-codingRNA-specific express values so I thought to use:
grep -f <list of ncRNAs contigs> <express file>
I made a file with ncRNAs contigs IDs which looks like this:
Singlet_51268
Singlet_63946
Singlet_70630
Singlet_72272
Singlet_60543
Contig11105
Singlet_18043
Singlet_64779
Singlet_50335
Singlet_39678
Singlet_21655
Singlet_5438
Singlet_6400
Contig4197
Singlet_17193
Singlet_55710
Singlet_70948
Singlet_25172
Singlet_65515
Singlet_30239
Singlet_54617
Singlet_11188
Contig14540
Since my ncRNAs are 577, I expect to end up with a .xprs file with 577 rows but I ended up with a .xprs file of 701 Contigs.
So I have 124 Contigs that do not correspond to my ncRNAs.
How could I pull out ncRNAs-specific values? I tried playing around with grep but I can't fix it.
Any suggestions?
THanks
it worked perfectly. Thankls for the right and fast answer!
Please use
grep -wFf <list>
. It will be much faster given a long list.