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samtools sort -o out.bam in.bam
open: No such file or directory
[bam_sort_core] fail to open file out.bam

I recently came across bbmap. When to use it ?

*****WARNING: Query v300043428L4C001R0481272249 is marked as paired, but its mate does not occur next to it in your BAM file.  Skipping.

How to filter out host reads from paired-end fastq files?

How to fix this warning, it occurs while installing AutoConTAMPR dependencies

Warning (mostly harmless): No library found for -lstaden-read

htsjdk.samtools.SAMException: Could not find dictionary next to reference file file:///data/sata_data/workshop/wsu29/Parivartan/snakemake_germline_legacy/references/GRCh38.primary_assembly.genome.fa

Hi, I wanted to know how to calculate illumina read length 

How to check if the line begin with "#" or ">" etc in Raku aka perl6