...
Putting this all together and linking to the index directory, we have this. Go ahead and execute this from the command line – it will be fast.
| Code Block | ||||
|---|---|---|---|---|
| ||||
ln -s -f $WORK/archive/reference/bt2/mirbase.v20 mb20 bowtie2 --local -N 1 -L 16 -x mb20/hairpin_cDNA_hsa.fa -U fq/human_mirnaseq.fastq.gz -S human_mirnaseq.sam |
...
Now you should have a human_mirnaseq.sam file that you can examine using whatever commands you like. An example alignment looks like this (note this is one alignment record, although it has been broken up below for readability).
| Code Block | ||
|---|---|---|
| ||
TUPAC_0037_FC62EE7AAXX:2:1:2607:1430#0/1 0 hsa-mir-302b 50 22 3S20M13S * 0 0
TACGTGCTTCCATGTTTTANTAGAAAAAAAAAAAAG ZZFQV]Z[\IacaWc]RZIBVGSHL_b[XQQcXQcc
AS:i:37 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:16G3 YT:Z:UU |
...