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Count reads at specific gene features

First of all, you need gene coordinates. You can retrieve them in GTF format from GENCODE or other sources. Next, extract TSS and TES +/- 2kb windows from each gene, taking in mind that genes can be ...
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how to retain reads with low mapping quality (MAPQ) scores when using samtools view -q

Looking at the samtools view docs, I believe that you need to also set the -p flag if you want to retain "filtered" reads in the file and simply have them ...
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Aligning scRNA-seq fastq to .bam without cell barcodes

The linked dataset is based on the Smart-seq2 technology. This is a plate-based assay in which individual cells are first sorted into individual wells of a microwell plate via FACS. The cells are then ...
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