Comments (5)
EC is mainly for debugging. It is also used for some functionality of bfc, but not by default. Generally, if the first integer is 0, it means the read has been corrected. In this case, the string in the format of 0_a:h_b_l:h_0
, where a
is the number of k-mers not present in the solid k-mer hash table (ideally 0), h
is the max heap size in correction (smaller is better), b
is 1 if and only if no raw k-mers are solid (in this case, the first k-mer is found by changing one base in a brute-force way), l
is the number of corrections and h
is the number of high-quality corrections.
A positive first integer indicates a failure in correction. In this case, 2 means the read has an uncorrectable "N" and 3 means too many unsuccessful attempts.
from bfc.
Thanks for the explanation.
from bfc.
I also see a lot of ec:Z:4
and ec:Z:5
... possibly some more numbers.
Can you tell me what these are refering to?
thanks.
from bfc.
My last answer is inaccurate on ec:Z:e when e is non-zero. This part of code is more accurate.
from bfc.
ok, .. thanks.
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Related Issues (16)
- Seg fault/double free or corruption HOT 5
- bfc with MiSeq data? HOT 2
- phred33 to 64 encoding change
- Segfault HOT 10
- Provide summary information
- Document the meaning of -R (refine error-corrected reads)
- How does bfc assign quality scores? HOT 3
- Segmentation fault HOT 5
- BFC-ht versus BFC-bf HOT 1
- Read counter not incrementing HOT 3
- Memory consuming HOT 1
- code for arXiv evaluation table HOT 3
- drop reads containing specific set of kmers HOT 2
- Please tag a new stable release HOT 2
- bfc strips pairing info HOT 6
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