7.4 years ago by
thank you for your kind reply.
my reads are look like:
G6H7M2K02GSJ6M rank=0000448 x=2668.5 y=2204.0 length=101
G6H7M2K02IOEII rank=0001256 x=3441.0 y=1256.0 length=47
G6H7M2K02I46FY rank=0001789 x=3632.0 y=1612.0 length=61
in each read,hindIII cut site present somewhere in between.
and theoretically each read should be mapped at two different locations (either on the same chromosome or at different chromosomes).
I am a new one in this field [NGS data analysis] and now i am looking the same task in bowtie2 but unable to fix parameters in bowtie2
I used this command for bowtie1 and did not get desire out put
./bowtie2 < reference data base> -f <query> --all <outputfile>
I am expecting result something like that:
G6H7M2K01C5MVF, 75..19 of 345 and Chr4, 5564653..5564709 of 18585056 (52/57 ident)
75 TTCCCCCATCAAGAAATAGAACTGACTAATCCTAAGTCAAAGGGTCGAAAAACCCAA 19
5564653 TTCTCCCATCAAGAAATAGAACTGACTAATCCTAAGTCAAAGAGTCAAGAAACTCAA 5564709
explanation::: 75 to 19 position of read id G6H7M2K01C5MVF of length 345 mapped with chromosome 4 at 5564653 and 5564709 and rest of positions of read are matched on same chromosome at 5564536 and 5564622
G6H7M2K01C5MVF, 212..125 of 345 and Chr4, 5564536..5564622 of 18585056 (82/89 ident)
212 TATCCATTCTTATTCGATCACAGCGAGGGAGCAAGTCAAAATAGAAAAACTCACATTCATTGGGTTTAGGGATAATCAGGCTCGA-ACT 125
5564536 TATCTATTCTTATTCGATCACAGCGAGGAAGCAAGTTAAAATAGAAAAACTCACATTTATTGGGTTTAGGGATAATCAGGC--GACACT 5564622
waiting for your kind reply,