add note about samtools fastq
@@ -137,6 +137,7 @@ void bamtofastq_help(void) {
cerr << "\tIf you want to create a single, interleaved FASTQ file " << endl;
cerr << "\tfor paired-end data, you can just write both to /dev/stdout:" << endl << endl;
cerr << "\tbedtools bamtofastq -i x.bam -fq /dev/stdout -fq2 /dev/stdout > x.ilv.fq" << endl << endl;
+ cerr << "\tAlso, the samtools fastq command has more fucntionality and is a useful alternative." << endl << endl;
exit(1);
}
