Users can select from the link below the SeqCode command binary to run in Mac OS-X environments:
List of SeqCode binary files (Catalina/mac osx 19.6.0)
(gcc Apple LLVM version 10.0.1 (clang-1001.0.46.4))
List of SeqCode binary files (Mojave/mac osx 18.7.0)
(gcc Apple clang version 12.0.0 (clang-1200.0.32.28))
Benchmark on a comprenhensive dataset of 25 ChIP-seq experiments including outputs and info messages:
(1/4) List of experiments:
[ChIP-seq from mouse]
GSE79606
Beringer M, Pisano P, Di Carlo V, Blanco E et al. EPOP Functionally
Links Elongin and Polycomb in Pluripotent Stem Cells. Mol Cell 2016 Nov
17;64(4):645-658. PMID: 27863225
GSM2098958 H3K4me3 replicate 1 H3K4me3_mESC
GSM2098952 H3K27me3 H3K27me3_mESC
GSM2098948 Suz12 replicate 1 Suz12_mESC
GSM2098946 C17orf96 replicate 2 Epop_mESC
GSM2430240 Jarid2 replicate 1 Jarid2_mESC
-----------------
GSE67868
Morey L, Santanach A, Blanco E, Aloia L et al. Polycomb Regulates Mesoderm Cell
Fate-Specification in Embryonic Stem Cells through Activation and Repression Mechanisms.
Cell Stem Cell 2015 Sep 3;17(3):300-15. PMID: 26340528
GSM1657387 ESC Mel18 [ChIP-seq] Mel18_ESC
-----------------
GSE67868
Morey L, Santanach A, Blanco E, Aloia L et al. Polycomb Regulates Mesoderm
Cell Fate-Specification in Embryonic Stem Cells through Activation and Repression
Mechanisms. Cell Stem Cell 2015 Sep 3;17(3):300-15. PMID: 26340528
GSM2610616 ChIP_HA-Cbx6_R1 Cbx6_mESC
GSM2610619 ChIP_Cbx7 Cbx7_mESC
-----------------
GSE99530
Mas G, Blanco E, Ballaré C, Sansó M et al. Promoter bivalency favors an open chromatin
architecture in embryonic stem cells. Nat Genet 2018 Oct;50(10):1452-1462. PMID: 30224650
GSM2645501 ChIP_Mll2_WT MLL2_mESC
GSM2645511 ChIP_H3K36me3_WT H3K36me3_mESC
GSM2645513 ChIP_H3K27ac_WT H3K27ac_mESC
GSM2645503 ChIP_Pol2Ser5P_WT Ser5P_mESC
GSM2645515 ChIP_CTCF_WT CTCF_mESC
GSM2645505 ChIP_IgG_WT IgG_mESC
GSM2645509 ChIP_Ring1b_WT Ring1B_mESC
[ChIP-seq from human]
GSE135623
Jain P, Ballare C, Blanco E, Vizan P et al. PHF19 mediated regulation of
proliferation and invasiveness in prostate cancer cells. Elife 2020 Mar 10;9.
PMID: 32155117
GSM4023634 ChIPseq_PHF19_CTR PHF19_DU145
GSM4023636 ChIPseq_EZH2_CTR EZH2_DU145
GSM4023638 ChIPseq_SUZ12_CTR SUZ12_DU145
GSM4023640 ChIPseq_H3K27me3_CTR H3K27me3_DU145
GSM4023642 ChIPseq_INPUT_CTR INPUT_DU145
GSM4023643 ChIPseq_MTF2_CTR MTF2_DU145
-----------------
GSE131286
Sánchez-Molina S, Figuerola-Bou E, Blanco E, Sánchez-Jiménez M et al. RING1B recruits
EWSR1-FLI1 and cooperates in the remodeling of chromatin necessary for Ewing sarcoma
tumorigenesis. Sci Adv 2020 Oct;6(43). PMID: 33097530
GSM3768754 ChIPseq_RING1B_Replicate1 RING1B_EwS
GSM3768756 ChIPseq_INPUTforRING1B_Replicate1 INPUT_EwS
GSM3768758 ChIPseq_H2Aub1_Replicate1 H2AUb1_EwS
GSM4616796 ChIPseq_EWSR1-FLI1 FLI1_EwS
(2/4) Outputs and progress reports (Catalina binaries):
-
Output folders
-
Info messages
(3/4) Outputs and progress reports (Mojave binaries):
-
Output folders
-
Info messages
(4/4) Perl script automatizing the benchmarking:
-
Perl script (Catalina)
-
Perl script (Mojave)
-
README
Please, find further information about SeqCode standalone release on the following links:
- The SeqCode source code full distribution is accessible from GitHub at:
https://github.com/eblancoga/seqcode
- Details about how to setup the SeqCode applications in your computer:
[SETUP]
- Basic description of the SeqCode command line program usage:
[USAGE]
- List of SeqCode commands furnished with examples:
[COMMANDS]
- Definition of genome data file formats:
[FORMATS]