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AStra:测序数据对癌细胞进行数字核型分析
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py:4个
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2021-05-18
13:28:10
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AStra:用于细胞系快速鉴定的非整倍性光谱(数字核型分析) 动机:对细胞系遗传漂移和交叉污染的广泛关注,迫切需要将其认证为科学数据的基本质量控制。 当前用于认证的遗传技术非常耗时,并且需要特定的文献标准和实验室规程。 考虑到全基因组测序(WGS)数据很容易获得的事实,基于读取深度(RD)的计算分析已经可以估算细胞系的遗传概况。 AStra是一个基于Python的软件,可以从原始WGS读数中从头估计基因组范围的非整倍性谱。 它是一个简单,易于使用且免费的工具,可提供有关细胞系验证的染色体非整倍性的基本信息。 AStra提供了一个分析和可视化平台,可在不同细胞系/菌株之间快速轻松地进行比较。 我们建议AStra对使用癌细胞系的科学数据进行快速首过质量评估。 内容 要求 python> = 3.6.5 pysam> = 0.12 下载 cd ~ git clone https://gi
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AStra:测序数据对癌细胞进行数字核型分析 (183个子文件)
K562_GSM2054698_SRR3144864_ChipSeq.ordered_Chromosomal_Anueploidy.bed 16KB
CAL51_GSM1693027_SRR2035173_ChIPSeq_Input_hg19_CK_bowtie2_default.sorted_Chromosomal_Anueploidy.bed 11KB
VCap_ENCFF273KUS_ENCFF466WDC_merged_Input_hg19_CK_bowtie2_default_rmdup.removed.blackList.Region.bedtools_Chromosomal_Anueploidy.bed 10KB
PC3_GSM1917731_32.sorted_Chromosomal_Anueploidy.bed 9KB
SKBR3_GSM2258810.sorted_Chromosomal_Anueploidy.bed 9KB
MDA-MB-468_GSE85158_R1_GSM2258900_Input_rmdup.removed.blackList.Region.bedtools.sorted_Chromosomal_Anueploidy.bed 8KB
T47D_GSE23893_GSM589247.sorted_Chromosomal_Anueploidy.bed 8KB
22Rv1_ENCSR933UGQ_ENCFF745ZXO_ENCFF868MWO_merged_hg19_CK_bowtie2_default_rmdup.removed.blackList.Region.bedtools_Chromosomal_Anueploidy.bed 7KB
MOLT-4_GSE79288hg19_CK_bowtie2_default_rmdup.removed.blackList.Region.bedtools_Chromosomal_Anueploidy.bed 7KB
SUM159_SRR1692389_hg19_CK_bowtie2_default_sorted_Chromosomal_Anueploidy.bed 7KB
A427_Chromosomal_Anueploidy.bed 6KB
H82_Chromosomal_Anueploidy.bed 6KB
697_GSE79873_GSM2107713_Input_rmdup.removed.blackList.Region.bedtools_Chromosomal_Anueploidy.bed 6KB
MDA-MB-231_GSE85158_R1_GSM2258864_Input.sorted_Chromosomal_Anueploidy.bed 6KB
LnCap_SRR2566839_hg19_CK_bowtie2_default.sorted_Chromosomal_Anueploidy.bed 6KB
SK-N-SH_GSE90683_GSM2664362_Input_rmdup.removed.blackList.Region.bedtools_Chromosomal_Anueploidy.bed 5KB
IMR32_Chromosomal_Anueploidy.bed 5KB
HepG2_Chromosomal_Anueploidy.bed 5KB
CHP212_Chromosomal_Anueploidy.bed 4KB
HG01879_Chromosomal_Anueploidy.bed 4KB
HG00119_Chromosomal_Anueploidy.bed 3KB
HG00096_Chromosomal_Anueploidy.bed 3KB
PC3_GSM1917731_32.sorted_Aneuploidy_Spectrum.bed 828B
SKBR3_GSM2258810.sorted_Aneuploidy_Spectrum.bed 828B
A427_Aneuploidy_Spectrum.bed 796B
VCap_ENCFF273KUS_ENCFF466WDC_merged_Input_hg19_CK_bowtie2_default_rmdup.removed.blackList.Region.bedtools_Aneuploidy_Spectrum.bed 794B
K562_GSM2054698_SRR3144864_ChipSeq.ordered_Aneuploidy_Spectrum.bed 782B
MDA-MB-468_GSE85158_R1_GSM2258900_Input_rmdup.removed.blackList.Region.bedtools.sorted_Aneuploidy_Spectrum.bed 768B
MOLT-4_GSE79288hg19_CK_bowtie2_default_rmdup.removed.blackList.Region.bedtools_Aneuploidy_Spectrum.bed 766B
LnCap_SRR2566839_hg19_CK_bowtie2_default.sorted_Aneuploidy_Spectrum.bed 766B
MDA-MB-231_GSE85158_R1_GSM2258864_Input.sorted_Aneuploidy_Spectrum.bed 766B
T47D_GSE23893_GSM589247.sorted_Aneuploidy_Spectrum.bed 764B
H82_Aneuploidy_Spectrum.bed 750B
CHP212_Aneuploidy_Spectrum.bed 750B
HepG2_Aneuploidy_Spectrum.bed 745B
IMR32_Aneuploidy_Spectrum.bed 734B
SUM159_SRR1692389_hg19_CK_bowtie2_default_sorted_Aneuploidy_Spectrum.bed 733B
CAL51_GSM1693027_SRR2035173_ChIPSeq_Input_hg19_CK_bowtie2_default.sorted_Aneuploidy_Spectrum.bed 721B
SK-N-SH_GSE90683_GSM2664362_Input_rmdup.removed.blackList.Region.bedtools_Aneuploidy_Spectrum.bed 721B
22Rv1_ENCSR933UGQ_ENCFF745ZXO_ENCFF868MWO_merged_hg19_CK_bowtie2_default_rmdup.removed.blackList.Region.bedtools_Aneuploidy_Spectrum.bed 720B
697_GSE79873_GSM2107713_Input_rmdup.removed.blackList.Region.bedtools_Aneuploidy_Spectrum.bed 720B
HG01879_Aneuploidy_Spectrum.bed 720B
HG00119_Aneuploidy_Spectrum.bed 719B
HG00096_Aneuploidy_Spectrum.bed 701B
README.md 6KB
697_GSE79873_GSM2107713_Input_rmdup.removed.blackList.Region.bedtools_GenomeRD.png 92KB
K562_GSM2054698_SRR3144864_ChipSeq.ordered_GenomeRD.png 86KB
K562_GSM2054698_SRR3144864_ChipSeq.ordered_GenomeAneuploidyWithChrsMarkers.png 85KB
MOLT-4_GSE79288hg19_CK_bowtie2_default_rmdup.removed.blackList.Region.bedtools_GenomeRD.png 79KB
VCap_ENCFF273KUS_ENCFF466WDC_merged_Input_hg19_CK_bowtie2_default_rmdup.removed.blackList.Region.bedtools_GenomeRD.png 79KB
22Rv1_ENCSR933UGQ_ENCFF745ZXO_ENCFF868MWO_merged_hg19_CK_bowtie2_default_rmdup.removed.blackList.Region.bedtools_GenomeRD.png 78KB
SUM159_SRR1692389_hg19_CK_bowtie2_default_sorted_GenomeRD.png 77KB
VCap_ENCFF273KUS_ENCFF466WDC_merged_Input_hg19_CK_bowtie2_default_rmdup.removed.blackList.Region.bedtools_GenomeAneuploidyWithChrsMarkers.png 76KB
K562_GSM2054698_SRR3144864_ChipSeq.ordered_GenomeAneuploidy_Segments.png 76KB
PC3_GSM1917731_32.sorted_GenomeRD.png 76KB
MOLT-4_GSE79288hg19_CK_bowtie2_default_rmdup.removed.blackList.Region.bedtools_GenomeAneuploidyWithChrsMarkers.png 76KB
MDA-MB-468_GSE85158_R1_GSM2258900_Input_rmdup.removed.blackList.Region.bedtools.sorted_GenomeRD.png 76KB
PC3_GSM1917731_32.sorted_GenomeAneuploidyWithChrsMarkers.png 73KB
SK-N-SH_GSE90683_GSM2664362_Input_rmdup.removed.blackList.Region.bedtools_GenomeRD.png 73KB
MDA-MB-468_GSE85158_R1_GSM2258900_Input_rmdup.removed.blackList.Region.bedtools.sorted_GenomeAneuploidyWithChrsMarkers.png 71KB
VCap_ENCFF273KUS_ENCFF466WDC_merged_Input_hg19_CK_bowtie2_default_rmdup.removed.blackList.Region.bedtools_GenomeAneuploidy_Segments.png 70KB
MOLT-4_GSE79288hg19_CK_bowtie2_default_rmdup.removed.blackList.Region.bedtools_GenomeAneuploidy_Segments.png 70KB
T47D_GSE23893_GSM589247.sorted_GenomeRD.png 69KB
697_GSE79873_GSM2107713_Input_rmdup.removed.blackList.Region.bedtools_GenomeAneuploidyWithChrsMarkers.png 69KB
H82_GenomeRD.png 68KB
SUM159_SRR1692389_hg19_CK_bowtie2_default_sorted_GenomeAneuploidyWithChrsMarkers.png 67KB
SUM159_SRR1692389_hg19_CK_bowtie2_default_sorted_GenomeAneuploidy_Segments.png 66KB
PC3_GSM1917731_32.sorted_GenomeAneuploidy_Segments.png 66KB
T47D_GSE23893_GSM589247.sorted_GenomeAneuploidyWithChrsMarkers.png 65KB
H82_GenomeAneuploidyWithChrsMarkers.png 65KB
LnCap_SRR2566839_hg19_CK_bowtie2_default.sorted_GenomeRD.png 64KB
697_GSE79873_GSM2107713_Input_rmdup.removed.blackList.Region.bedtools_GenomeAneuploidy_Segments.png 64KB
MDA-MB-468_GSE85158_R1_GSM2258900_Input_rmdup.removed.blackList.Region.bedtools.sorted_GenomeAneuploidy_Segments.png 63KB
CAL51_GSM1693027_SRR2035173_ChIPSeq_Input_hg19_CK_bowtie2_default.sorted_GenomeRD.png 62KB
22Rv1_ENCSR933UGQ_ENCFF745ZXO_ENCFF868MWO_merged_hg19_CK_bowtie2_default_rmdup.removed.blackList.Region.bedtools_GenomeAneuploidyWithChrsMarkers.png 61KB
SKBR3_GSM2258810.sorted_GenomeRD.png 60KB
HepG2_GenomeRD.png 59KB
T47D_GSE23893_GSM589247.sorted_GenomeAneuploidy_Segments.png 58KB
LnCap_SRR2566839_hg19_CK_bowtie2_default.sorted_GenomeAneuploidyWithChrsMarkers.png 58KB
SKBR3_GSM2258810.sorted_GenomeAneuploidyWithChrsMarkers.png 56KB
HepG2_GenomeAneuploidyWithChrsMarkers.png 55KB
IMR32_GenomeRD.png 55KB
H82_GenomeAneuploidy_Segments.png 55KB
CAL51_GSM1693027_SRR2035173_ChIPSeq_Input_hg19_CK_bowtie2_default.sorted_GenomeAneuploidyWithChrsMarkers.png 54KB
22Rv1_ENCSR933UGQ_ENCFF745ZXO_ENCFF868MWO_merged_hg19_CK_bowtie2_default_rmdup.removed.blackList.Region.bedtools_GenomeAneuploidy_Segments.png 54KB
IMR32_GenomeAneuploidyWithChrsMarkers.png 53KB
CAL51_GSM1693027_SRR2035173_ChIPSeq_Input_hg19_CK_bowtie2_default.sorted_GenomeAneuploidy_Segments.png 53KB
SK-N-SH_GSE90683_GSM2664362_Input_rmdup.removed.blackList.Region.bedtools_GenomeAneuploidyWithChrsMarkers.png 52KB
K562_GSM2054698_SRR3144864_ChipSeq.ordered_GenomeAneuploidy.png 52KB
LnCap_SRR2566839_hg19_CK_bowtie2_default.sorted_GenomeAneuploidy_Segments.png 52KB
A427_GenomeRD.png 51KB
MDA-MB-231_GSE85158_R1_GSM2258864_Input.sorted_GenomeRD.png 50KB
CHP212_GenomeRD.png 50KB
SKBR3_GSM2258810.sorted_GenomeAneuploidy_Segments.png 50KB
A427_GenomeAneuploidyWithChrsMarkers.png 49KB
CHP212_GenomeAneuploidyWithChrsMarkers.png 48KB
MDA-MB-231_GSE85158_R1_GSM2258864_Input.sorted_GenomeAneuploidyWithChrsMarkers.png 47KB
SK-N-SH_GSE90683_GSM2664362_Input_rmdup.removed.blackList.Region.bedtools_GenomeAneuploidy_Segments.png 47KB
HepG2_GenomeAneuploidy_Segments.png 46KB
IMR32_GenomeAneuploidy_Segments.png 46KB
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