i mapped reads to my transcrpitome assemblied from those reads.
there is a record in the sam file
HWI-ST397_0000:5:1101:19602:2158#ATCTCG 20 UN57620 131 25 95M *
0 0 GTTGATCTGAGAGTAGCAGATGCCCTCAATCTTCACATCCTTGGGCACTTTGGCGCCCATGTCA
GTGTCAGAGGGCTGGATGCTCGTGAAGGTGC BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB XT:A:U NM:i:5 X0:i:1 X1:i:0 X
M:i:5 XO:i:0 XG:i:0 MD:Z:11C3C11G63C1T1
i think the flag=20, = 16+4, 16 means reverse, 4 means unmapped, but i found it can mapped from 131 on UN57620
the mapped sequences are here, not reverse
>UN057620
CCCGCTATAGCCATGATCCTAGCTTGAAAATCTCGTTGCG
GCAAAATTTATGCTTTGTCGGCGGATAAAGGAGGGTAAGT
GTATGTTTTGTTTACAAAGAGGAATCAAATCAGTGTAGGA
CGACAGTCTAGTTGATCTGAGCGTACCAGATGCCCTCGAT #UN057620
GTTGATCTGAGAGTAGCAGATGCCCTCAAT #read
CTTCACATCCTTGGGCACTTTGGCGCCCATGTCAGTGTCA #UN057620
GAGGGCTGGATGCTCGTGAA#read
CTTCACATCCTTGGGCACTTTGGCGCCCATGTCAGTGTCA #UN057620
GAGGGCTGGATGCTCGTGAAGGTGC#read
there is a record in the sam file
HWI-ST397_0000:5:1101:19602:2158#ATCTCG 20 UN57620 131 25 95M *
0 0 GTTGATCTGAGAGTAGCAGATGCCCTCAATCTTCACATCCTTGGGCACTTTGGCGCCCATGTCA
GTGTCAGAGGGCTGGATGCTCGTGAAGGTGC BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB XT:A:U NM:i:5 X0:i:1 X1:i:0 X
M:i:5 XO:i:0 XG:i:0 MD:Z:11C3C11G63C1T1
i think the flag=20, = 16+4, 16 means reverse, 4 means unmapped, but i found it can mapped from 131 on UN57620
the mapped sequences are here, not reverse
>UN057620
CCCGCTATAGCCATGATCCTAGCTTGAAAATCTCGTTGCG
GCAAAATTTATGCTTTGTCGGCGGATAAAGGAGGGTAAGT
GTATGTTTTGTTTACAAAGAGGAATCAAATCAGTGTAGGA
CGACAGTCTAGTTGATCTGAGCGTACCAGATGCCCTCGAT #UN057620
GTTGATCTGAGAGTAGCAGATGCCCTCAAT #read
CTTCACATCCTTGGGCACTTTGGCGCCCATGTCAGTGTCA #UN057620
GAGGGCTGGATGCTCGTGAA#read
CTTCACATCCTTGGGCACTTTGGCGCCCATGTCAGTGTCA #UN057620
GAGGGCTGGATGCTCGTGAAGGTGC#read
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