Analysis typeReference Alignment
OEZ014554
Analysis typeReference Alignment
OEZ014553
Analysis typeDe Novo Assembly
OEZ014551
Analysis typeDe Novo Assembly
OEZ014550
Analysis typeDe Novo Assembly
OEZ014548
Analysis typeDe Novo Assembly
OEZ014549
Analysis typeOther
OEZ014547
DescriptionTo process raw data, reads containing adapter or ploy-N were removed to generate clean reads. Further filtration according to the calculated Q20, Q30 and GC content resulted in high-quality clean reads, which were then aligned to reference human genome GRCh38 using the BWA program (version 0.7.15). The MACS2 package(version 2.2.9.1)was used for peak-calling from the BAM files with q-value < 0.05. HOMER (version 4.11) was applied to the generated peak file and the genome fasta for motif analysis. Peaks were annotated using the annotatePeaks.pl function. For defining differentially accessible peaks, peak files of each sample were first merged using BEDTools (version 2.28.0). The counts of the reads over the bed were then determined for each sample using the multicov function from BEDTools. Finally, differentially accessible peaks were assessed using DESeq2 (version v1.42.0).
Analysis typeOther
OEZ014525
DescriptionThe raw reads were decoded by ST_BarcodeMap (version 0.0.1), filtered adapter sequence by Fastp, and then aligned to the reference genome GRCh38.p12(Human) via STAR. Mapped reads were annotated, then calculated by HandleBam(version 1.0.0). The raw matrix was converted into the bin50-level matrix (i.e., 25*25um) by the Seurat R package(version 4.2.0). For quality control, the median number of gene types per bin50 for all chips should be over 500.
Analysis typeOther
OEZ013918
DescriptionThe raw reads were decoded by ST_BarcodeMap (version 0.0.1), filtered adapter sequence by Fastp, and then aligned to the reference genome GRCh38.p12(Human) via STAR. Mapped reads were annotated, then calculated by HandleBamz(version 1.0.0). Single-cell segmentation of Stereo-seq data is performed by a self-written algorithm.
Analysis typeOther
OEZ013917