How to extract unique mapped results from Bowtie2 bam results?
I used samtools view -bq 1 WG.bam > unique.bam
However, my results contain 54792 lines, why it is not 42097?
After I have the subset of those reads, how can I extract them from sam or bam file to create a new fastq format file? Can anybody offer some code to do so?
“samopen] SAM header is present: 84 sequences.
60291 reads; of these:
60291 (100.00%) were unpaired; of these:
2788 (4.62%) aligned 0 times
42097 (69.82%) aligned exactly 1 time
15406 (25.55%) aligned >1 times
95.38% overall alignment rate”
SRR029237.10 16 4 21793833 42 242M * 0 0 TTCCCAGTGTCTAGAATGTGGCATGCCCACAACAAATTCTAGCTGAAGGAATCAGCAAGGAGATGTTATGGAGCTCTACCAAAATACTAACCCAGAACTTGAGACATGGTCAGTCATGAGAATTTCCACTACGCTCTGCTTCTGTGATGTTAATTTTTATATTAACATATAAAATAATGGCATATATAGATTTTGAAGTGTGTGCTAATGGCATAAAATTGCCCTCATAAATAAATGAAGTC =C1BF9<<=8==<4<C:6:7@::==-@D;<5>7,?D9A;5<<==:=C:B6?<<:;<=C=C<<;;;<B;;=C=8<<<<:;C(6CG<;<;9A,@D9<;C<=D<==;=;9<C9<<===<<<;9;B/AE=D==<8;;:<=<;=<C;:=<<=6<;A=C&09DH<:=<C=C:<;7<(6CG84==<C==9<<=<==;(6CG;=D=<<==<<<=;B:6><6:’5BF2;5)>B:<;=.AE=-@E;;;B=;= AS:i:-8 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:23G108A109 YT:Z:UU
SRR029237.11 0 17 62886136 1 37M1I159M * 0 0 TCTCTAGATCNCAAAATCCCTTTTAGAATCCAACTCTGGGGTGGCACCAAGATCAGCAGAACCTCCATTTCCTCCTCTCTTTTCCCAAACCTTATTATGAAAGCCCCACATGGAACCATGTCAGGGCTGCAAGTGAAGCCATTCAACCTTTTTCCCCCCATCAAAAAAATTGGAGAACTATAATGTGCATAAAGTGC 1<;=8;==76!8FB4&<B>)FB4&58=48@8C=8<;=EA3#9C=8=B=B<<<38;<<7<C=C=<?6;FB2C=<C=;;4;GC7+FB0EA.B;C=.B::3<A=’8EA3#5=<:@7@8C=:8=:;;FA/=8;<>5=<7B:1D=<D=6>5C=GC8.%GC91)”92=GB92,'”@9B<7<@;:<:9C<;8=;13;EA.<3=< AS:i:-9 XS:i:-9 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:10A185 YT:Z:UU
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