Gene counting

AI Ane Iturbide
MS Mayra L. Ruiz Tejeda Segura
CN Camille Noll
KS Kenji Schorpp
IR Ina Rothenaigner
ER Elias R. Ruiz-Morales
GL Gabriele Lubatti
AA Ahmed Agami
KH Kamyar Hadian
AS Antonio Scialdone
MT Maria-Elena Torres-Padilla
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Unique molecular identifier (UMI) counts were obtained using the kallisto (version 0.46.0) bustools (version 0.39.3) pipeline55. First, mouse transcriptome and genome (release 98) fasta and gtf files were downloaded from the Ensembl website, and 10X barcodes list version 3 was downloaded from the bustools website. We built an index file with the ‘kallisto index’ function with default parameters. Then, pseudoalignment was done using the ‘kallisto bus’ function with default parameters and the barcodes for 10X version 3. The BUS files were corrected for barcode errors with ‘bustools correct’ (default parameters), and a gene count matrix was obtained with ‘bustools count’ (default parameters). To estimate the tbGFP read counts, we used the tbGFP sequence available from GenBank (ID ASW25889.1) and followed the same procedure.

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