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Open Access Highly Accessed Research article

Computational approaches for isoform detection and estimation: good and bad news

Claudia Angelini1*, Daniela De Canditiis2 and Italia De Feis1

Author Affiliations

1 Istituto per le Applicazioni del Calcolo, CNR, Naples, Italy

2 Istituto per le Applicazioni del Calcolo, CNR, Rome, Italy

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BMC Bioinformatics 2014, 15:135  doi:10.1186/1471-2105-15-135

Published: 9 May 2014

Additional files

Additional file 1:

Figure S1. F-measure in Set-up 1 for 100 bp-PE. Panels A (upper left) and B (upper right) depict F-measure versus the sequencing depth for each compared method when the alignment is annotation driven using CA and IA, respectively. Panels C (bottom left) and D (bottom right) are analogous to Panels A and B, when the alignment is data driven. The figure refers to Set-up 1 and 100 bp-PE. Within each panel, methods in Mode 1 are depicted with continuous line, methods in Mode 2 with dashed line, methods in Mode 3 with dotted line. When the alignment is annotation driven, the same annotation provided during the alignment was used for Mode 1 and 2.

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Additional file 2:

Figure S2. F-measure in Set-up 1 for 75 bp-PE. Analogous to Additional file 1: Figure S1, but for Set-up 1 and 75 bp-PE.

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Additional file 3:

Figure S3. F-measure in Set-up 1 for 50 bp-PE. Analogous to Additional file 1: Figure S1, but for Set-up 1 and 50 bp-PE.

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Additional file 4:

Figure S4. F-measure in Set-up 1 for 100 bp-SE. Analogous to Additional file 1: Figure S1, but for Set-up 1 and 100 bp-SE.

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Additional file 5:

Figure S5. True Positives and False Positives in Set-up 1 for 20M 100 bp-PE. Panels A (upper left) and B (upper right) depict TP (coral) and FP (aquamarine) bars for the compared methods when the alignment is annotation driven (CA and IA, respectively). Panels C (bottom left) and D (bottom right) are analogous to Panels A and B, when the alignment is data driven. The figure refers to Set-up 1 and 20M 100 bp-PE. The true number of expressed transcripts (i.e., 3726) is added as dashed horizontal line to each panel. The difference between the TP and the horizontal line represents the FN.

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Additional file 6:

Figure S6. True Positives and False Positives in Set-up 1 for 20M 100 bp-SE. Analogous to Additional file 5: Figure S5, but for Set-up 1 and 20M 100 bp-SE.

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Additional file 7:

Figure S7. True Positives and False Positives in Set-up 1 for 0.25M 100 bp-PE. Analogous to Additional file 5: Figure S5, but for Set-up 1 and 0.25M 100 bp-PE.

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Additional file 8:

Figure S8. True Positives and False Positives in Set-up 1 for 0.25M 100 bp-SE. Analogous to Additional file 5: Figure S5, but for Set-up 1 and 0.25M 100 bp-PE.

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Additional file 9:

Figure S9. Precision and Recall bar-plot in Set-up 2 for 75 bp-PE. Analogous to Figure 2, but for Set-up 2 for 60M 75 bp-PE.

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Additional file 10:

Figure 10. Precision and Recall bar-plot in Set-up 2 for 50 bp-PE. Analogous to Figure 2, but for Set-up 2 for 60M 50 bp-PE.

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Additional file 11:

Figure S11. Recall bar-plot versus isoform abundance in Set-up 2 for 60M 75 bp-PE. Analogous to Figure 5, but for Set-up 2 for 60M 75 bp-PE.

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Additional file 12:

Figure S12. Recall bar-plot versus isoform abundance in Set-up 2 for 60M 50 bp-PE. Analogous to Figure 5, but for Set-up 2 for 60M 50 bp-PE.

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Additional file 13:

Figure S13. Precision, Recall and F-measure when introducing thresholds (Set-up 2). Analogous to Figure 12, but for Set-up 2, 60M 75 bp-PE and the alignment with CA.

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Additional file 14:

Figure S14. True Positives and False Positives in Set-up 2 for 60M 75 bp-PE. Panels A (upper left) and B (upper right) depict TP (coral) and FP (aquamarine) bars for the compared methods when the alignment is annotation driven (CA and IA, respectively). Panels C (bottom left) and D (bottom right) are analogous to Panels A and B, when the alignment is data driven. The figure refers to Set-up 2 and 60M 75 bp-PE. The true number of expressed transcripts (i.e., 17032) is added as dashed horizontal line to each panel. The difference between the TP and the horizontal line represents the FN.

Format: PDF Size: 133KB Download file

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Additional file 15:

Table S1. E1, E2 and E3 in Set-up 1 with annotation driven alignment (CA) for 20M 100 bp-PE. Median, 3rd Quartile and maximum value observed for error indexes E1, E2 and E3 in Set-up 1, 20M PE reads of 100 bp. Tables are divided in blocks, where the left block is for methods used in Mode 1, middle block is for methods used in Mode 2, right block is for methods used in Mode 3. Upper rows refer to E1, middle ones refer to E2, bottom ones refer to E3. CA was provided during the alignment.

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Additional file 16:

Table S2. E1, E2 and E3 in Set-up 1 with annotation driven alignment (IA) for 20M 100 bp-PE. Analogous to Additional file 15: Table S1, but with IA provided during the alignment.

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Additional file 17:

Table S3. E1, E2 and E3 in Set-up 1 with annotation driven alignment (CA) for 0.25M 100 bp-PE. Analogous to Additional file 15: Table S1, but for 0.25M PE reads.

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Additional file 18:

Table S4. E1, E2 and E3 in Set-up 1 with annotation driven alignment (IA) for 0.25M 100 bp-PE. Analogous to Additional file 15: Table S1, but for 0.25M PE reads and with IA provided during the alignment.

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Additional file 19:

Table S5. E1, E2 and E3 in Set-up 1, with data driven alignment and CA for 20M 100 bp-PE. Analogous to Additional file 15: Table S1, but with data driven alignment. CA was provided in Mode 1 and Mode 2.

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Additional file 20:

Table S6. E1, E2 and E3 in Set-up 1, with data driven alignment and IA for 20M 100 bp-PE. Analogous to Additional file 15: Table S1, but with data driven alignment. IA was provided in Mode 1 and Mode 2.

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Additional file 21:

Table S7. E1, E2 and E3 in Set-up 1, with data driven alignment and CA for 0.25M 100 bp-PE. Analogous to Additional file 19: Table S5, but for 0.25M PE reads.

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Additional file 22:

Table S8. E1, E2 and E3 in Set-up 1, with data driven alignment and IA for 0.25M 100 bp-PE. Analogous to Additional file 20: Table S6, but for 0.25M PE reads.

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Additional file 23:

Table S9. E1, E2 and E3 in Set-up 1 with annotation driven alignment (CA) for 20M 100 bp-SE. Analogous to Additional file 15: Table S1, but for 20M SE reads.

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Additional file 24:

Table S10. E1, E2 and E3 in Set-up 1 with annotation driven alignment (IA) for 20M 100 bp-SE. Analogous to Additional file 17: Table S2, but for 20M SE reads.

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Additional file 25:

Table S11. E1, E2 and E3 in Set-up 1 with annotation driven alignment (CA) for 0.25M 100 bp-SE. Analogous to Additional file 17: Table S3, but for 0.25M SE reads.

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Additional file 26:

Table S12. E1, E2 and E3 in Set-up 1 with annotation driven alignment (IA) for 0.25M 100 bp-SE. Analogous to Additional file 18: Table S4, but for 0.25M SE reads.

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Additional file 27:

Table S13. E1, E2 and E3 in Set-up 1, with data driven alignment and CA for 20M 100 bp-SE. Analogous to Additional file 19: Table S5, but for 20M SE reads.

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Additional file 28:

Table S14. E1, E2 and E3 in Set-up 1, with data driven alignment and IA for 20M 100 bp-SE. Analogous to Additional file 20: Table S6, but for 20M SE reads.

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Additional file 29:

Table S15. E1, E2 and E3 in Set-up 1, with data driven alignment and CA for 0.25M 100 bp-SE. Analogous to Additional file 21: Table S7, but for 025M SE reads.

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Additional file 30:

Table S16. E1, E2 and E3 in Set-up 1, with data driven alignment and IA for 0.25M 100 bp-SE. Analogous to Additional file 22: Table S8, but for 025M SE reads.

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Additional file 31:

Table S17. Statistics for E1, E2 and E3 in Set-up 2 with annotation driven alignment (CA) for 60M 75 bp-PE. Analogous to Additional file 15: Table S1, but for Set-up 2, 60M 75 bp-PE.

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Additional file 32:

Table S18. Statistics for E1, E2 and E3 in Set-up 2 with annotation driven alignment (IA) for 60M 75 bp-PE. Analogous to Additional file 17: Table S2, but for Set-up 2, 60M 75 bp-PE.

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Additional file 33:

Table S19. Statistics for E1, E2 and E3 in Set-up 2 with data driven alignment and CA for 60M 75 bp-PE. Analogous to Additional file 19: Table S5, but for Set-up 2, 60M 75 bp-PE.

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Additional file 34:

Table S20. Statistics for E1, E2 and E3 in Set-up 2 with data driven alignment and IA for 60M 75 bp-PE. Analogous to Additional file 20: Table S6, but for Set-up 2, 60M 75 bp-PE.

Format: XLS Size: 22KB Download file

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