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public data TCGA GTEx Tutorial

8.3 years ago shepherl 4.2k

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Comment: Ensembl 115 has been released! by eja.gsssssswwse.r.m • 0

Keeping up with Ensembls latest release ensures access to cutting-edge genomic information. For those balancing research and leisure, a mob…

Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k

Hi Rui Tang, The "buffer overflow detected" error in featureCounts usually stems from a corrupted or malformed GTF file, often due to tr…

Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k

Hi, The linear TMB plot with no clustering suggests your variant calls may lack sample-specific discrimination, likely due to filtering ap…

Answer: gene Set with high AUC score but no cells assigned to cell type by Kevin Blighe ★ 4.0k

Hi, You have correctly identified the issue: AUCell's automatic threshold selection is conservative by design, aiming for specificity to…

Answer: featureCounts -L: high unassigned:mapq fraction by Kevin Blighe ★ 4.0k

Hi Katarzyna, The discrepancy arises because your samtools stats were restricted to genic regions only, where alignments are typically o…

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Answer: DESeq2 design for haplotype MPRA

Answer: Suppress warning in RHDF5 write

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