Storing FASTQ as unaligned CRAM

I was updating my BAM to CRAM post spurred on by a recent comment and then I wondered whether I could store my FASTQ files as unaligned CRAM files to save space. I thought it wouldn’t be possible because the reads are unaligned and therefore we can’t make use of a reference to save space…

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Creating a coverage plot using BEDTools and R

One of my Top 10 posts is on creating a coverage plot using R. For that post I used CAGE data, which is a transcriptomic data set containing transcription start sites, and I used R exclusively for building a “coverage plot.” The main issue with that post was that the plots were density plots rather…

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Understanding the BAM flags

I’ve tried to explain the BAM flags to my colleagues and I think each time I have left them more confused. So perhaps I can do a better job of explaining BAM flags in writing. For this post, I will use this BAM file from the 1000 Genomes Project: NA18553.chrom11.ILLUMINA.bwa.CHB.low_coverage.20120522.bam.

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