New answers tagged bam
3
votes
Accepted
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 ...
- 96
2
votes
Accepted
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 ...
- 2,782
1
vote
Accepted
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 ...
- 36
Top 50 recent answers are included