(2024 )Cite this post
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We present SPLASH2, a quickly, scalable execution of SPLASH based upon an effective k-mer counting technique for controlled series variation detection in huge datasets from a vast array of sequencing innovations and biological contexts. We show biological discovery by SPLASH2 in single-cell RNA sequencing (RNA-seq) information and wholesale RNA-seq information from the Cancer Cell Line Encyclopedia, consisting of unannotated alternative splicing in cancer transcriptomes and delicate detection of circular RNA.
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The FASTQ declare the SS2 human muscle cells8 were downloaded from https://tabula-sapiens-portal.ds.czbiohub.org/. The ALS data3 were downloaded from the Sequence Read Archive (SRA) database (SRP185789). The FASTQ apply for the 671 cell lines in CCLE18 from main growths were downloaded from the SRA database (SRP186687). The circRNA benchmarking data10 were downloaded from the SRA database (SRP350843). The human recommendation genome T2T was downloaded from https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/analysis_set/chm13v2.0.fa.gz. The annotation apply for the human referral transcriptome UCSC GENCODEv35 CAT/Liftoff v2 was downloaded from https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/annotation/chm13.draft_v2.0.gene_annotation.gff3.
The SPLASH2 pipeline, in addition to in-depth guidelines and test information, is offered through a GitHub repository38. The software application variations utilized for the lead to the paper were as follows: STAR variation 2.7.5. a, zstd variation 1.5.4, BEDTools variation 2.25.0, R variation 4.1.2 and Python variation 3.9.7.
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Salzman, J., Gawad, C., Wang, P. L., Lacayo, N. & & Brown, P. O. Circular RNAs are the primary records isoform from numerous human genes in varied cell types. PLoS ONE 7, e30733 (2012 ).
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Chaung, K. et al. SPLASH: an analytical, reference-free genomic algorithm merges biological discovery. Cell 186, 5440– 5456 (2023 ).
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Ma, X. R. et al. TDP-43 quelches puzzling exon addition in the FTD– ALS gene UNC13A Nature 603, 124– 130 (2022 ).
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