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Kinfe Bankole edited this page Jul 17, 2024 · 32 revisions

Single GTF TranD

This data was computed from pairwise and full gene transcript complements in a single GTF file.

Two GTF TranD

This data was computed from pairwise comparisons between genes in two GTF files. Transcripts are compared for each gene pair.

Isoseq vs FLAIR

  • D. melanogaster PacBio FLAIR vs. IsoSeq3 cluster (Raw Data - pending) (IsoSeq3 cluster GTF) (FLAIR GTF) (Method) (TranD Output)

  • D. simulans PacBio FLAIR vs. IsoSeq3 cluster (Raw Data - pending) (IsoSeq3 cluster GTF) (FLAIR GTF) (Method) (TranD Output)

  • Wtc11 PacBio FLAIR vs. Isoseq3 (Raw Data - pending) (Consolidated IsoSeq3 cluster GTF) (Consolidated FLAIR GTF) (TranD Pairwise Distance File)

  • Z. mays B73v4 FLAIR vs. Isoseq3 (Raw Data - pending) (IsoSeq3 cluster GTF) (FLAIR GTF) (TranD Output)

  • C. elegans ONT FLAIR vs. Isoseq3 (Raw Data - pending) (IsoSeq3 cluster GTF) (FLAIR GTF) (TranD Output)

Transcript Model Map

  • Drosophila references (mel v sim) mapped to mel: Link
  • Drosophila references (mel v sim) mapped to sim: Link
  • Cross-Species Union: Link
  • Human (Ensembl vs. Refseq): Link

Other Files

  • The extracted transcript FASTA for five different Drosophila species (melanogaster, simulans, santomea, yakuba, serrata): Link

  • TranD 1GTF (gene mode) output run on the Ensembl vs. Refseq Union Reference created in the Transcript Model Map process: Link

TranD Runtime Chart

The below table contains more thorough runtimes for some of the above pre-computed output. Use this to predict how much memory/time and how many CPUs will be necessary for running TranD.

Annotation(s) Num Transcripts TranD Mode Num CPUs Max Memory Usage (kb) Time (hh:mm:ss)
Dmel 6.17 35255 1 GTF Gene 64 821.56 00:35:29
Dmel 6.17 35255 1 GTF Pairwise 64 1836.524 01:46:42
Single Refseq Annotation from Ensembl vs Refseq 165898 1 GTF Gene 64 4800.968 20:59:38
Ensembl vs Refseq – Chr 1 20492 vs 16075 2 GTF All 64 5123.724 14:50:06
Ensembl vs Refseq – Chr 2 17239 vs 12345 2 GTF All 64 4674.92 10:05:42
Ensembl vs Refseq – Chr 3 14700 vs 10404 2 GTF All 64 4452.216 09:00:18
Ensembl vs Refseq – Chr 4 9619 vs 7032 2 GTF All 64 3260.14 02:50:20
Ensembl vs Refseq – Chr 5 11193 vs 7115 2 GTF All 64 2431.02 02:29:16
Ensembl vs Refseq – Chr 6 10879 vs 8449 2 GTF All 64 2908.112 03:06:49
Ensembl vs Refseq – Chr 7 11091 vs 7844 2 GTF All 64 2638.476 02:52:26
Ensembl vs Refseq – Chr 8 9632 vs 6185 2 GTF All 64 2667.912 02:20:06
Ensembl vs Refseq – Chr 9 7943 vs 6995 2 GTF All 64 2228.436 02:17:33
Ensembl vs Refseq – Chr 10 8279 vs 7758 2 GTF All 64 3147.46 02:57:00
Ensembl vs Refseq – Chr 11 13978 vs 9358 2 GTF All 64 4039.156 06:33:35
Ensembl vs Refseq – Chr 12 13072 vs 8821 2 GTF All 64 3784.34 07:00:46
Ensembl vs Refseq – Chr 13 4297 vs 3423 2 GTF All 64 1093.372 00:21:28
Ensembl vs Refseq – Chr 14 8594 vs 5402 2 GTF All 64 2314.848 01:46:58
Ensembl vs Refseq – Chr 15 8613 vs 5505 2 GTF All 64 2133.12 01:37:37
Ensembl vs Refseq – Chr 16 11086 vs 6607 2 GTF All 64 2774.608 02:35:16
Ensembl vs Refseq – Chr 17 13815 vs 8632 2 GTF All 64 3617.92 06:44:39
Ensembl vs Refseq – Chr 18 4485 vs 3056 2 GTF All 64 1681.216 00:34:15
Ensembl vs Refseq – Chr 19 13770 vs 9007 2 GTF All 64 3008.044 03:30:06
Ensembl vs Refseq – Chr 20 5500 vs 4248 2 GTF All 64 1291.284 00:34:58
Ensembl vs Refseq – Chr 21 3017 vs 2019 2 GTF All 64 839.3 00:09:41
Ensembl vs Refseq – Chr 22 5002 vs 3618 2 GTF All 64 1386.016 00:31:48
Ensembl vs Refseq – Chr X 7286 vs 5145 2 GTF All 64 1592.66 00:49:38
Ensembl vs Refseq – Chr Y 826 vs 660 2 GTF All 64 330.416 00:00:39
Ensembl vs Refseq – Mitochondrial 37 vs 24 2 GTF All 64 181.876 00:00:07
Dmel vs Dsim Reference Comparison – Mapped to Mel 33794 vs 41352 2 GTF Minimum 64 6037.52 23:55:51
Dmel vs Dsim Reference Comparison – Mapped to Sim 39812 vs 25958 2 GTF Minimum 64 6575.252 22:55:20

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