Hello, I had a question related to the cell ranger --count function output. I ran --counts function on all 12 samples together, 6 of them were treatment and 6 were control. for example,
1013MJ1
1013MJ2
1013Saline1
1013Saline2
106MJ1
106MJ2
106Saline
106Saline2
113MJ-1
113MJ-2
113Saline1
113Saline2
I got bunch of outputs, and I am performing downstream analysis on raw_feature_bc_matrix.h5 using Seurat package in R. However, it seems like this file does not contain Sample information. I'm not sure which file they might be stored in, but I believe it might be stored in molecule_info.h5. I am not sure how to incorporate the Sample info into the count matrix for e.g raw_feature_bc_matrix.h5 file when I make a Seurat object. Can you help me figure out how I can put sample information in the Seurat object.
Below is the R script that I am using to read both files but molecule_info.h5 does not get read and gives me an error.
library(Seurat)
library(ggplot2)
library(tidyverse)
library(gridExtra)
library(SeuratDisk)
library(patchwork)
data_dir <- "/home/shamzar/Jianmei/Single_cell/yard/1013MJ1/outs/raw_feature_bc_matrix.h5"
h5 <- Read10X_h5(data_dir, use.names = TRUE, unique.features = TRUE)
nkdata <- CreateSeuratObject(counts = h5 , project = "NKproject", min.cells = 3, min.features = 200, assay = "RNA")
metadata_dir <- "/home/shamzar/Jianmei/Single_cell/yard/1013MJ1/outs/molecule_info.h5"
Mh5 <- Read10X_h5 (metadata_dir)
ERROR
Error in x$exists(name) : HDF5-API Errors:
error #000: H5L.c in H5Lexists(): line 845: unable to get link info
class: HDF5
major: Links
minor: Can't get value
error #001: H5L.c in H5L__exists(): line 2932: path doesn't exist
class: HDF5
major: Links
minor: Object already exists
error #002: H5Gtraverse.c in H5G_traverse(): line 848: internal path traversal failed
class: HDF5
major: Symbol table
minor: Object not found
error #003: H5Gtraverse.c in H5G__traverse_real(): line 579: can't look up component
class: HDF5
major: Symbol table
minor: Object not found
error #004: H5Gobj.c in H5G__obj_lookup(): line 1135: can't locate object
class: HDF5
major: Symbol table
minor: Object not found
error #005: H5Gstab.c in H5G__stab_lookup(): line 876: can't read message
class: HDF5
major: Symbol table
minor: Unrecognized message
error #006: H
I was able to load and make a seurat object for the raw_feature_bc_matrix.h5 file but it does not have the sample info. and when I try to load the molecule_info.h5 file it gives me and error. Once I have read this file I would also want to pull the sample info from this file and put it in my seurat object that I created using raw_feature_bc_matrix.h5.
