unaligned reads

[husamia]

LRA reports a message about the number of reads that were aligned and the total number of reads. The command

zcat reads.fastq.gz | lra align -ONT -t 16 -a hg19.fa - -p s > reads_lra2.sam
e.g.
lra aligned 14907 from 24253, 116M bases (403.1s).

How do I get the reads that did not align. i.e. in my case 9346 reads didn't align (38%)?

I did

samtools view -f 4 reads_lra2.sam | wc -l

284

counting reads from all the flags [0, 16, 2048, 2064, 4] i.e.:

for i in {16,0,2048,2064,4}; do echo flag: $i;samtools view -f $i reads_lra2.sam|wc -l;done

I get

flag: 16
12205
flag: 0
24768
flag: 2048
515
flag: 2064
301
flag: 4
284

There are only 284 unmapped reads (flag: 4).