update fix update docs.
@@ -78,12 +78,12 @@ end 1 and one for end 2.
When using this option, it is required that the BAM
file is sorted/grouped by the read name. This keeps the resulting records
in the two output FASTQ files in the same order. One can sort the BAM
- file by query name with ``samtools sort -n aln.bam aln.qsort``.
+ file by query name with ``samtools sort -n -o aln.qsort.bam aln.bam``.
.. code-block:: bash
- $ samtools sort -n aln.bam aln.qsort
+ $ samtools sort -n -o aln.qsort.bam aln.bam
$ bedtools bamtofastq -i aln.qsort.bam \
-fq aln.end1.fq \
