I am setting up continuous integration using GitHub Actions. One of the prerequisites (samtools) is most easily installed by conda. The standard way to use installed packages is to activate the cor...

I am using python/pysam to do analyze sequencing data. In its tutorial (pysam - An interface for reading and writing SAM files) for the command mate it says: 'This method is too slow for high-thro...

I have this program called samtools (version 1.3) that is used for manipulating the files that you get from DNA sequencing experiments. The downloaded program is contained in a folder. To set the ...

To give you a bit of context: I am trying to convert a sam file to bam samtools view -bT reference.fasta sequences.sam > sequences.bam which exits with the following error [E::sam_parse1] CI...

I've quickly realized that bioinformatics is not a subject which has its terms clearly defined and easily accessible. I have an apparent discrepancy with some of my results. I used samtools view -...

Lets say I had the following command running from the shell { samtools view -HS header.sam; # command1 samtools view input.bam 1:1-50000000; # command2 } | samtools view -bS - > output.bam # c...