Difference between revisions of "TXGP Data Description"
From Marcotte Lab
(→TXGP_XENLA_RNA_SA11024) |
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** ENGPU (''Engystomops pustulosus'' a.k.a. Túngara Frog or ''Physalaemus pustulosus''). | ** ENGPU (''Engystomops pustulosus'' a.k.a. Túngara Frog or ''Physalaemus pustulosus''). | ||
− | == | + | == Data pre-processing == |
+ | * Remove reads with any no-call('N' in Illumina fastq file; '.' in SOLiD csfasta file). | ||
+ | * Remove low-complex reads, with less than 4 letters('0123' for color space, 'ATGC' for base space). | ||
− | == | + | == TXGP data == |
+ | === TXGP_XENLA_BAC2k_SA09023 (SOLiDv2)=== | ||
− | == | + | === TXGP_XENLA_BAC5k_SA09023 (SOLiDv2) === |
− | == | + | === TXGP_XENTR_WG5k_SA09023 (SOLiDv2) === |
− | == | + | === TXGP_XENLA_WG1500_SA10026 (SOLiDv3) === |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | == | + | === TXGP_XENLA_RNA_SA11017 (SOLiDv3) === |
− | * | + | * SA11017_XENLA_Heart_JA11050v3BC10F3 (24.0M) |
− | * | + | * SA11017_XENLA_Heart_JA11050v3BC10F5 (23.4M) |
− | * | + | * SA11017_XENLA_Testis_JA11050v3BC04F3 (33.1M) |
− | * | + | * SA11017_XENLA_Testis_JA11050v3BC04F5 (32.4M) |
− | == | + | === TXGP_XENLA_RNA_SA11022 (SOLiDv3) === |
+ | * SA11022_XENLA_Egg_JA11015v4BC001F3 (19.3M) | ||
+ | * SA11022_XENLA_Egg_JA11015v4BC001F5 (19.4M) | ||
+ | * SA11022_XENLA_Stage24_JA11015v2BC13F3 (16.5M) | ||
+ | * SA11022_XENLA_Stage24_JA11015v2BC13F5 (16.6M) | ||
− | == TXGP_XENLA_RNA_SA11024 == | + | === TXGP_ENGPU_RNA_SA11022 (SOLiDv3) === |
+ | |||
+ | === TXGP_XENLA_RNA_SA11024 (SOLiDv3) === | ||
* SA11024_XENLA_Liver_JA11055v2BC12F3 (21.0M) | * SA11024_XENLA_Liver_JA11055v2BC12F3 (21.0M) | ||
* SA11024_XENLA_Liver_JA11055v2BC12F5 (22.0M) | * SA11024_XENLA_Liver_JA11055v2BC12F5 (22.0M) | ||
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* SA11024_XENLA_Stomach_JA11055v4BC003F3 (27.8M) | * SA11024_XENLA_Stomach_JA11055v4BC003F3 (27.8M) | ||
* SA11024_XENLA_Stomach_JA11055v4BC003F5 (29.1M) | * SA11024_XENLA_Stomach_JA11055v4BC003F5 (29.1M) | ||
+ | |||
+ | == Contributed Data == | ||
+ | We are looking for ''X. laevis'' RNA-seq data for building comprehensive gene models. | ||
+ | |||
+ | === Amin2011_XENLA_RNA_UNC (Illumina HiSeq)=== | ||
+ | Data from [http://www.unc.edu/~fconlon/ Frank Conlon lab] at University of North Carolina at Chapel Hill. | ||
+ | * Amin2011_XENLA_Stage38Heart_WT | ||
+ | * AMin2011_XENLA_Stage45Heart_CtrlMO | ||
---- | ---- | ||
[[Category:XenopusGenome]] | [[Category:XenopusGenome]] |
Revision as of 13:09, 21 June 2011
Naming convention
- Directory name: '(investigator)_(species code)_(sample type)_(SA#)'
- File name: '(SA#)_(species code)_(description)_(JA#,barcode,F3/F5/R3)'
- Species code
- XENLA (Xenopus laevis)
- XENTR (Xenopus tropicalis a.k.a. Silurana tropicalis)
- ENGPU (Engystomops pustulosus a.k.a. Túngara Frog or Physalaemus pustulosus).
Data pre-processing
- Remove reads with any no-call('N' in Illumina fastq file; '.' in SOLiD csfasta file).
- Remove low-complex reads, with less than 4 letters('0123' for color space, 'ATGC' for base space).
TXGP data
TXGP_XENLA_BAC2k_SA09023 (SOLiDv2)
TXGP_XENLA_BAC5k_SA09023 (SOLiDv2)
TXGP_XENTR_WG5k_SA09023 (SOLiDv2)
TXGP_XENLA_WG1500_SA10026 (SOLiDv3)
TXGP_XENLA_RNA_SA11017 (SOLiDv3)
- SA11017_XENLA_Heart_JA11050v3BC10F3 (24.0M)
- SA11017_XENLA_Heart_JA11050v3BC10F5 (23.4M)
- SA11017_XENLA_Testis_JA11050v3BC04F3 (33.1M)
- SA11017_XENLA_Testis_JA11050v3BC04F5 (32.4M)
TXGP_XENLA_RNA_SA11022 (SOLiDv3)
- SA11022_XENLA_Egg_JA11015v4BC001F3 (19.3M)
- SA11022_XENLA_Egg_JA11015v4BC001F5 (19.4M)
- SA11022_XENLA_Stage24_JA11015v2BC13F3 (16.5M)
- SA11022_XENLA_Stage24_JA11015v2BC13F5 (16.6M)
TXGP_ENGPU_RNA_SA11022 (SOLiDv3)
TXGP_XENLA_RNA_SA11024 (SOLiDv3)
- SA11024_XENLA_Liver_JA11055v2BC12F3 (21.0M)
- SA11024_XENLA_Liver_JA11055v2BC12F5 (22.0M)
- SA11024_XENLA_Lung_JA11055v2BC11F3 (35.1M)
- SA11024_XENLA_Lung_JA11055v2BC11F5 (36.7M)
- SA11024_XENLA_Stomach_JA11055v4BC003F3 (27.8M)
- SA11024_XENLA_Stomach_JA11055v4BC003F5 (29.1M)
Contributed Data
We are looking for X. laevis RNA-seq data for building comprehensive gene models.
Amin2011_XENLA_RNA_UNC (Illumina HiSeq)
Data from Frank Conlon lab at University of North Carolina at Chapel Hill.
- Amin2011_XENLA_Stage38Heart_WT
- AMin2011_XENLA_Stage45Heart_CtrlMO