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| Name | Modified | Size | Downloads / Week |
|---|---|---|---|
| Parent folder | |||
| README.md | 2022-04-15 | 2.1 kB | |
| Mouse4-ERR3320871.tar.gz | 2022-04-15 | 39.9 MB | |
| Mouse3-ERR3320855.tar.gz | 2022-04-15 | 38.0 MB | |
| Mouse2-DRR205677.tar.gz | 2022-04-15 | 31.5 MB | |
| Mouse1-DRR205674.tar.gz | 2022-04-15 | 32.2 MB | |
| Human8-SRR7536920.tar.gz | 2022-04-15 | 42.7 MB | |
| Human7-SRR315334.tar.gz | 2022-04-15 | 38.0 MB | |
| Human6-SRR315323.tar.gz | 2022-04-15 | 38.9 MB | |
| Human5-SRR307903.tar.gz | 2022-04-15 | 37.9 MB | |
| Human4-ERR2403203.tar.gz | 2022-04-15 | 39.9 MB | |
| Human3-SRR10517380.tar.gz | 2022-04-15 | 45.4 MB | |
| Human2-SRR387662.tar.gz | 2022-04-15 | 42.2 MB | |
| Human1-SRR307911.tar.gz | 2022-04-15 | 43.4 MB | |
| GRCm38.fa | 2022-04-15 | 2.8 GB | |
| GRCm38.gtf | 2022-04-15 | 413.4 MB | |
| GRCh38.fa | 2022-04-15 | 3.2 GB | |
| GRCH38.gtf | 2022-04-15 | 416.9 MB | |
| Totals: 17 Items | 7.2 GB | 0 | |
====================
Files Description
====================
The files GRCh38.fa and GRCH38.gtf are the Homo sapiens reference genome and reference transcriptome used to generate the alignments and evaluate the assemblers in the Tiglon paper, and GRCm38.fa and GRCm38.gtf are the Mus musculus reference genome and reference transcriptome.
Note that these four files could also be dowloaded from this website: http://genome.ucsc.edu/cgi-bin/hgTables
In each compressed file you may see 8 files in GTF format, where each compressed file corresponds to a dataset and the GTF files are the assembled results of the tested assemblers in the Tiglon paper.
For instance, the file Human1-SRR307911.tar.gz means in the corresponding decompressed file you may get the assemblies of each assembler on the data SRR307911.
Tiglon.gtf is the assembled results of Tiglon based on both Hisat2 and Star alignments.
stringtie_hisat.gtf is the assembled results of stringtie2 based on the Hisat2 alignment.
stringtie_star.gtf is the assembled results of stringtie2 based on the Star alignment.
stringtie_merge_0.1.gtf is the assembled results of "stringtie --merge".
stringtie_MergedAlignment.gtf is the assembled results of stringtie2 based on the merged-alignements produce by "samtools merge MergedAlignment.bam Hisat.bam Star.bam"
scallop_hisat.gtf is the assembled results of scallop based on the Hisat2 alignment.
scallop_star.gtf is the assembled results of scallop based on the Star alignment.
scallop_MergedAlignment.gtf is the assembled results of scallop based on the merged-alignements produce by "samtools merge MergedAlignment.bam Hisat.bam Star.bam"
Besides, in some folder you may see the Hisat.bam and Star.bam, which are the alignments files generated by Hisat2 and Star aligners.
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Please noting that all the above Hisat2 alignments are generated with its option --dta.
In the Hisat2 manual, the option "--dta" means "reports alignments tailored for transcript assemblers”.
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