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

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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