{"id":114,"date":"2016-06-18T11:07:27","date_gmt":"2016-06-18T15:07:27","guid":{"rendered":"http:\/\/sys4seq.com\/?page_id=5"},"modified":"2022-06-08T17:02:43","modified_gmt":"2022-06-08T21:02:43","slug":"home","status":"publish","type":"page","link":"https:\/\/sys4seq.com\/","title":{"rendered":"Home"},"content":{"rendered":"
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Computing<\/h2>\n<\/div>\n
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Cluster and AWS.<\/p>\n<\/div>\n

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Bioinformatics<\/h2>\n<\/div>\n
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RNA-seq and proteomics<\/p>\n<\/div>\n

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Genomics<\/h2>\n<\/div>\n
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WGS and WES<\/p>\n<\/div>\n

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Building<\/h2>

a real-time big data pipeline<\/h4><\/div><\/div>\n<\/div>\n<\/div><\/div><\/div>\n
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Spatial gene expression data analysis on Cluster : 10X Genomics, Space Ranger<\/a><\/h4>\n
\n\tPosted on Ashok Dinasarapu<\/a><\/span> Analysis<\/a> Omics<\/a> Transcriptomics<\/a><\/span>\n<\/div>\n\n
Running spaceranger as cluster mode that uses Sun Grid Engine (SGE) as queuing. There are 2 steps to analyze Spatial RNA-seq data. Step 1: spaceranger mkfastq demultiplexes raw base call (BCL) files generated by Illumina sequencers into FASTQ files. Step 2: spaceranger count takes FASTQ files from spaceranger mkfastq and performs alignment, filtering, barcode counting,<\/div>\nread more<\/a>\n