After identifying lncRNA in P.generosa, Steven asked that I generate an tissue-specific expression/count matrix (GitHub Issue). Looking through the documentation for StringTie, I decided that StringTie would work for this. The overall approach:

Use tissue-specifc BAMs from HISAT2 alignments
Use “canonical” lncRNA GTF representing all lncRNAs found across all tissues as input to StringTie.
Use StringTie’s expression estimation feature to generate read coverage and expression (FPKM) for each lncRNA.
Use StringTie’s Python script (prepDE.py3) to generate tissue/sample-specific count matrix.

This was all run on Raven, using a Jupyter Notebook. Links below:

20230504-pgen-lncRNA-expression.ipynb

Jupyter Notebook (NB Viewer):

20230502-pgen-lncRNA-identification.ipynb

RESULTS

This produced ballgown expression files, as well as a transcript read count matrix with a column for each tissue/sample. I’m only linking directly to the final matrix file due to the number of samples and redundant ballgown files/structure. To view the organization of the output directory, see the directory tree below

Output folder:

20230504-pgen-lncRNA-expression/

Transcript count matrix (CSV)

20230504-pgen-lncRNA-expression/transcript_count_matrix.csv

transcript_id	ctenidia	gonad	heart	juvenile	larvae
MSTRG.1.1	34	16	13	93	6
MSTRG.2.1	18	5	2	9	2
MSTRG.3.1	15	9	48	171	60
MSTRG.22.1	4	24	7	27	22
MSTRG.9.1	3	133	1	1681	245
MSTRG.11.1	88	123	77	144	95
MSTRG.12.1	3	81	12	47	50
MSTRG.25.1	6	47	8	0	1
MSTRG.27.1	4	79	9	12	4

Directory tree

├── [4.0K]  ctenidia
│   ├── [3.9M]  ctenidia-pgen-lncRNA-stringtie.gtf
│   ├── [137K]  e2t.ctab
│   ├── [997K]  e_data.ctab
│   ├── [  10]  i2t.ctab
│   ├── [  48]  i_data.ctab
│   └── [1.2M]  t_data.ctab
├── [316K]  gene_count_matrix.csv
├── [4.0K]  gonad
│   ├── [137K]  e2t.ctab
│   ├── [1002K]  e_data.ctab
│   ├── [3.9M]  gonad-pgen-lncRNA-stringtie.gtf
│   ├── [  10]  i2t.ctab
│   ├── [  48]  i_data.ctab
│   └── [1.2M]  t_data.ctab
├── [4.0K]  heart
│   ├── [137K]  e2t.ctab
│   ├── [990K]  e_data.ctab
│   ├── [3.9M]  heart-pgen-lncRNA-stringtie.gtf
│   ├── [  10]  i2t.ctab
│   ├── [  48]  i_data.ctab
│   └── [1.2M]  t_data.ctab
├── [4.0K]  juvenile
│   ├── [137K]  e2t.ctab
│   ├── [1.0M]  e_data.ctab
│   ├── [  10]  i2t.ctab
│   ├── [  48]  i_data.ctab
│   ├── [3.9M]  juvenile-pgen-lncRNA-stringtie.gtf
│   └── [1.2M]  t_data.ctab
├── [4.0K]  larvae
│   ├── [137K]  e2t.ctab
│   ├── [1001K]  e_data.ctab
│   ├── [  10]  i2t.ctab
│   ├── [  48]  i_data.ctab
│   ├── [3.9M]  larvae-pgen-lncRNA-stringtie.gtf
│   └── [1.2M]  t_data.ctab
└── [409K]  transcript_count_matrix.csv

5 directories, 32 files