Basic Question: How to get appropriate pDATA structure in monocle from cufflinks/cuffnorm
0
0
Entering edit mode
@alexandriapinto1-13151
Last seen 6.1 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 • 992 views
ADD COMMENT

Login before adding your answer.

Traffic: 695 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6