I know that the read order of xxx_F3.csfasta and xxx_F3_QV.qual are the same, but I can't find any information that describes how the read order of xxx_F3.csfasta and xxx_R3.csfasta are related. I'd appreciate any pointers to documentation that describe the order relationship.
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Originally posted by smarkel View PostI know that the read order of xxx_F3.csfasta and xxx_F3_QV.qual are the same, but I can't find any information that describes how the read order of xxx_F3.csfasta and xxx_R3.csfasta are related. I'd appreciate any pointers to documentation that describe the order relationship.
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The files I'm using are from AB's site (http://solidsoftwaretools.com/gf/project/ecoli2x50/) and aren't sorted. I looked at Rosalind_20080729_2_Chris5_F3.csfasta.zip and Rosalind_20080729_2_Chris5_R3.csfasta.zip. My understanding is that the sorting happens when the reads are mapped. Maybe the posted files aren't representative.
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Originally posted by smarkel View PostThe files I'm using are from AB's site (http://solidsoftwaretools.com/gf/project/ecoli2x50/) and aren't sorted. I looked at Rosalind_20080729_2_Chris5_F3.csfasta.zip and Rosalind_20080729_2_Chris5_R3.csfasta.zip. My understanding is that the sorting happens when the reads are mapped. Maybe the posted files aren't representative.
Take a look at these reads from real data:
Code:>1_6_55_F3 T01100000000201002010120012300200011000100.01101131 >1_6_64_F3 T01203010110102003000000101100111000010100.01100131 >1_6_69_F3 T01031320200103032011110221111112110020111.11111131 >1_6_97_F3
>%d_%d_%d_F3
where %d stands for some integer. It is sorted by the right-most integer, then middle integer, then left-most integer. The equivalent read (the mate) in the R3 file will be
>%d_%d_%d_R3
The "Rosalind" file follows the same pattern:
Code:>469_26_42_F3 T12113310031232112221003120021221223320222122212122 >469_26_379_F3 T31202223003310000130302323312223212011000010033200 >469_26_540_F3 T11012313031030123033113130100223110001231232303210 >469_26_560_F3
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Thank you. Yes, you're right. Both files are individually sorted. I should have worded my original question differently. I expected xxx_F3.csfasta and xxx_R3.csfasta to have the same number of entries, with the nth entry in the F3 file being the mate of the nth entry in the R3 file. What does it mean for a paired read's mate to not exist?
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Originally posted by smarkel View PostThank you. Yes, you're right. Both files are individually sorted. I should have worded my original question differently. I expected xxx_F3.csfasta and xxx_R3.csfasta to have the same number of entries, with the nth entry in the F3 file being the mate of the nth entry in the R3 file. What does it mean for a paired read's mate to not exist?
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