I've been following multiple tutorials trying to get started with monocle and cufflinks. I'm running the software using hisat2 ->cuffquant->cuffnorm -> monocle as suggested by the getting started portion of the monocle manual. When I display featureData/fData from my newCellDataSet I get exactly what is expected.
However when I look at my pData, or the data that I inputted from cuffnorm/samples.table, this is the data I get:
sample_id file total_mass internal_scale external_scale
1_0 testSoftware/file_sorted1.bam 664056 1.58363 1
10_0 testSoftware/file_sorted10.bam 850312 0.695295 1
11_0 testSoftware/file_sorted11.bam 715739 1.26876 1
12_0 testSoftware/file_sorted12.bam 706052 1.41086 1
13_0 testSoftware/file_sorted13.bam 792907 1.29823 1
14_0 testSoftware/file_sorted14.bam 256.717 0.0018186 1
15_0 testSoftware/file_sorted15.bam 719395 1.26392 1
16_0 testSoftware/file_sorted16.bam 228307 0.212768 1
17_0 testSoftware/file_sorted17.bam 579919 0.997461 1
18_0 testSoftware/file_sorted18.bam 594039 0.96488 1
19_0 testSoftware/file_sorted19.bam 721492 1.55507 1
However the vignette says that the data should look like:
## Library Well Time cell_id Cells.in.Well Debris Clump
## T0_CT_A01 SCC10013_A01 A01 T0_CT_ T0_CT_A01 1 FALSE FALSE
## T0_CT_A03 SCC10013_A03 A03 T0_CT_ T0_CT_A03 1 FALSE FALSE
## T0_CT_A05 SCC10013_A05 A05 T0_CT_ T0_CT_A05 1 FALSE FALSE
## T0_CT_A06 SCC10013_A06 A06 T0_CT_ T0_CT_A06 1 FALSE FALSE
## T0_CT_A07 SCC10013_A07 A07 T0_CT_ T0_CT_A07 1 FALSE FALSE
## T0_CT_A08 SCC10013_A08 A08 T0_CT_ T0_CT_A08 1 FALSE FALSE
## Unusual.Shape Control Time.1 Cell.Type Media Raw.Fragments
## T0_CT_A01 FALSE FALSE 0 HSMM GM
## T0_CT_A03 FALSE FALSE 0 HSMM GM
## T0_CT_A05 FALSE FALSE 0 HSMM GM
## T0_CT_A06 FALSE FALSE 0 HSMM GM
## T0_CT_A07 FALSE FALSE 0 HSMM GM
## T0_CT_A08 FALSE FALSE 0 HSMM GM
## Mapped.Fragments Raw.Reads Aligned.Reads Expression.File
## T0_CT_A01 1958074 NA NA NA
## T0_CT_A03 1930722 NA NA NA
## T0_CT_A05 1452623 NA NA NA
## T0_CT_A06 2566325 NA NA NA
## T0_CT_A07 2383438 NA NA NA
T0_CT_A08 1472238 NA NA NA
## num_genes_expressed Pseudotime State
## T0_CT_A01 9770 7.200 1
## T0_CT_A03 9180 2.716 1
## T0_CT_A05 8528 2.272 1
## T0_CT_A06 7096 6.461 1
## T0_CT_A07 7590 3.402 1
## T0_CT_A08 7702 20.300
I dont understand what I am doing wrong and my advisor cant figure it out either. Is there another step I have to do to make that data look like that? Any help would be so appreciated.
