Basic Question: How to get appropriate pDATA structure in monocle from cufflinks/cuffnorm
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@alexandriapinto1-13151
Last seen 3.6 years ago

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. 

cufflinks monocle • 561 views
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