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I have used GMAP to mapping my RNA-seq data to the reference genome with parameter ( -f samse -z sense_force -t 5 -n 0 --cross-species --allow-close-indels 0 ) to get SMA output ,but I have many multi-map like this(in format of sam without collumn 10 and collumn 11):
PB.9993.8 16 ta_iwgsc_3b_v1_10412403 337 0 3412H119M1140N127M1D76M1I33M * 0 0 ..... MD:Z:202A5C34T2^C109 NH:i:3 HI:i:1 NM:i:5 SM:i:40 XQ:i:0 X2:i:0 XO:Z:UT XS:A:- XT:Z:GT-AG,0.99,1.00,[email protected]_iwgsc_3b_v1_10529945@17271 XG:Z:M
PB.9993.8 16 ta_iwgsc_3b_v1_10529945 12068 0 333M1251N1799M86N75M103N192M172N252M105N553M76N208M356H * 0 0 ... MD:Z:333T385A605C345C918G363T11T445 NH:i:3 HI:i:1 NM:i:7 SM:i:40 XQ:i:0 X2:i:0 XO:Z:UT XS:A:- XT:Z:GT-AG,0.99,1.00,[email protected]_iwgsc_3b_v1_10529945@17271XG:Z:M
It seems a hard clipped mapping. Now I want to do the alternative analysis, So I want filter out the Hard Clips with only one mapping. Is there any parameter in gmap can do this?
Thanks a lot for any reply!
PB.9993.8 16 ta_iwgsc_3b_v1_10412403 337 0 3412H119M1140N127M1D76M1I33M * 0 0 ..... MD:Z:202A5C34T2^C109 NH:i:3 HI:i:1 NM:i:5 SM:i:40 XQ:i:0 X2:i:0 XO:Z:UT XS:A:- XT:Z:GT-AG,0.99,1.00,[email protected]_iwgsc_3b_v1_10529945@17271 XG:Z:M
PB.9993.8 16 ta_iwgsc_3b_v1_10529945 12068 0 333M1251N1799M86N75M103N192M172N252M105N553M76N208M356H * 0 0 ... MD:Z:333T385A605C345C918G363T11T445 NH:i:3 HI:i:1 NM:i:7 SM:i:40 XQ:i:0 X2:i:0 XO:Z:UT XS:A:- XT:Z:GT-AG,0.99,1.00,[email protected]_iwgsc_3b_v1_10529945@17271XG:Z:M
It seems a hard clipped mapping. Now I want to do the alternative analysis, So I want filter out the Hard Clips with only one mapping. Is there any parameter in gmap can do this?
Thanks a lot for any reply!
