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- Frazee AC, Langmead B, Leek JT. ReCount: a multi-experiment resource of analysis-ready RNA-seq gene count datasets. BMC Bioinformatics 12:449
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The table on the previous page includes count tables and ExpressionSets created by running Myrna with the truncate=35 option, while the table on this page provides the count tables and ExpressionSets created by running Myrna without the truncation option. Datasets not included on this page were not affected by the truncation (i.e., their reads were no more than 35bp). The -v 3 Bowtie option (rather than -v 2 ) was used for the studies containing reads of length 50bp or longer to allow for 3 mismatches rather than only 2 in the alignment step.
Datasets, without truncation
Study | PMID | Species | Number of biological replicates | Read Length(s), bp | Number of uniquely aligned reads | ExpressionSet | Count table |
bodymap | not published, but publicly available here | human | 19 | 50, 75, 100 | 1,732,952,136 | link | link |
cheung | 20856902 | human | 41 | 50 | 761,310,848 | link | link |
montgomery | 20220756 | human | 60 | 36 | *881,304,874 | link | link |
pickrell | 20220758 | human | 69 | 35, 46 | *881,304,874 | link | link |
wang | 18978772 | human | 22 | 32, 36 | 222,319,658 | link | link |
trapnell | 20436464 | mouse | 4 | 76 | 64,075,691 | link | link |
yang | 20363980 | mouse | 1 | 36 | 27,647,780 | link | link |
bottomly | 21455293 | mouse | 21 | 70, 76 | 287,321,756 | link | link |
hammer | 20452967 | rat | 8 | 50 | 144,944,741 | link | link |
modencodeworm | 19181841 | worm | 46 | 36, 76 | 1,253,144,777 | link | link |
modencodefly | 21179090 | fly | 147 (technical)** 30 (biological) |
75, 76 | 1,756,719,388 | link | link |
**The modENCODE fly study contained 147 replicates and 30 developmental stages. Replicates within a developmental stage were technical and may be pooled during data analysis if desired.
Code used for this table
Commands passed to MyrnaR code used to create ExpressionSets (requires Bioconductor and additional files)