We’d like to have some clarification on the error code in the scrap.fasta, following
make.contigs(file=batch_file, oligos=oligos_file, bdiffs=0, pdiffs=0, checkorient=t, insert=25, trimoverlap=f, allfiles=0)
We found most of the error codes falling into these 3 categories;
What exactly do they mean ? Our guess is that, i.e., for f(b)(bf), a barcode was found in the first direction, but not a primer, so it checked the second direction. In the second direction it could not find a barcode so the read failed with the “total error code” bf
Thanks for your help !
M00347_15_000000000-JNGG2_1_1102_3501_21352 | f(b)(bf) ee=7.17938e-06 fbdiffs=1000(noMatch), rbdiffs=1000(noMatch) fpdiffs=1000(noMatch), rpdiffs=1000(noMatch)
M00347_15_000000000-JNGG2_1_1102_18979_12812 | b(bf)(bf) ee=1.82457e-06 fbdiffs=1000(noMatch), rbdiffs=1000(noMatch) fpdiffs=1000(noMatch), rpdiffs=1000(noMatch)
M00347_15_000000000-JNGG2_1_1101_16655_7263 | bf(bf)(bf) ee=2.48811e-06 fbdiffs=1000(noMatch), rbdiffs=1000(noMatch) fpdiffs=1000(noMatch), rpdiffs=1000(noMatch)