Description of output header

[sklages]

Hi,
I'd like to see how/if error correction worked for my dataset.
Can you explain what e.g.
ec:Z:3
ec:Z:0_0:10_0_0:0_0
ec:Z:0_31:1_0_0:0_0
ec:Z:0_6:6_1_5:4_0
means? What about unaltered header lines?

thanks,
Sven

[lh3]

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.

[sklages]

Thanks for the explanation.

[sklages]

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.

[lh3]

My last answer is inaccurate on ec:Z:e when e is non-zero. This part of code is more accurate.

[sklages]

ok, .. thanks.