Output files

Output file: _gene.out

This file is created per sample and includes the TPM values at gene or transcript level.

The columns are:

1. Gene_Id
2. Chr
3. Length (Transcript length)
4. Count_Reads (Reads assigned to the gene or transcript)
5. TPM (TPM value for the gene or transcript)
6. Length of non-overlapping gene exons
7. Reads assigned to the non-overlapping gene exons
8. TPM for the non-overlapping gene exons
9. Length of non-overlapping gene introns
10. Reads assigned to the non-overlapping gene introns
11. TPM for the non-overlapping gene introns
12. Exon_Length (Sum of all exonic regions)
13. Exon_Count_Reads (All reads assigned to the exonic regions)
14. Exon_TPM (TPM for all the exonic regions)
15. Intron_Length (Sum of all intronic regions)
16. Intron_Count_Reads (All reads assigned to the intronic regions)
17. Intron_TPM (TPM for all the intronic regions)

Output file: _transcript.out

This file is created per sample and includes the TPM values at gene or transcript level.

The columns are:

1. Gene_Id
2. Transcript_Id (Not present in the gene file)
3. Chr
4. Length (Transcript length)
5. Count_Reads (Reads assigned to the gene or transcript)
6. TPM (TPM value for the gene or transcript)
7. Exon_Length (Sum of all exonic regions)
8. Exon_Count_Reads (All reads assigned to the exonic regions)
9. Exon_TPM (TPM for all the exonic regions)
10. Intron_Length (Sum of all intronic regions)
11. Intron_Count_Reads (All reads assigned to the intronic regions)
12. Intron_TPM (TPM for all the intronic regions)

Output file: _[gene|transcript].ent

This file is per sample and includes the TPM values for each exon and intron at gene or transcript level.

The columns are:

1. Gene_Id
2. Transcript_Id (Not present in the gene file)
3. Chr
4. Type ( feature type: exon or intron)
5. Type_Number (the consecutive number starting from 1)
6. start (feature start coordinate)
7. end (feature end coordinate)
8. Length (feature length)
9. Count_Reads (reads assigned to the feature)
10. TPM (TPM calculated for the feature)

Output file: [genes|transcripts]_data_per_samples.txt

This file is created when multiple BAM files are processed from a directory. It includes the TPM values for exonic region and intronic region calculated for each gene or transcript for each sample.

The columns are (using the same names than before):

1. Gene_Id
2. Transcript_Id (Not present in the gene file)
3. sample1_exon
4. sample1_intron
5. sample2_exon
6. sample2_intron