Trimmomatic log file format explanation?

Question

[willbrown]

Hi,

I have recently used Trimmomatic and included the -trimlog argument and been trying to make sense of the log.txt file generated. I have looked at the official manual and I'm still not sure. I've pasted in a small portion of my log file below:

HWI-D00461:137:C9H2FACXX:4:1101:1187:1993 2:N:0:CTTGTA 101 0 101 0
HWI-D00461:137:C9H2FACXX:4:1101:1117:1997 1:N:0:CTTGTA 101 0 101 0
HWI-D00461:137:C9H2FACXX:4:1101:1117:1997 2:N:0:CTTGTA 101 0 101 0
HWI-D00461:137:C9H2FACXX:4:1101:1229:1999 1:N:0:CTTGTA 48 0 48 53
HWI-D00461:137:C9H2FACXX:4:1101:1229:1999 2:N:0:CTTGTA 77 0 77 24
HWI-D00461:137:C9H2FACXX:4:1101:1162:2000 1:N:0:CTTGTA 101 0 101 0
HWI-D00461:137:C9H2FACXX:4:1101:1162:2000 2:N:0:CTTGTA 101 0 101 0
HWI-D00461:137:C9H2FACXX:4:1101:1393:1965 1:N:0:CTTGTA 69 1 70 31
HWI-D00461:137:C9H2FACXX:4:1101:1393:1965 2:N:0:CTTGTA 101 0 101 0
HWI-D00461:137:C9H2FACXX:4:1101:1305:1965 1:N:0:CTTGTA 100 1 101 0

The area I'm specifically confused about is the very end of each line. I've assumed the numbers separated by colons are coordinates on the flow cells and the '1/2:N:0:CTTGTA' specifies which read (either 1 or 2) it is. The area '48 0 48 53', I am assuming shows the number of overall bases as well as bases removed; as in this example it would be 48 overall bases remaining and 53 bases removed. Is this correct? Any help is appreciated.

Many thanks,

Will.

Answer 1

[GenoMax]

See explanation here: How to find/decipher Trimmomatic Output

HWI-D00461:137:C9H2FACXX:4:1101:1229:1999 2:N:0:CTTGTA 77 0 77 24

The last 4 space-delimited numbers are the

surviving length (77), surviving first base(0), surviving last base(77) and amount trimmed (24) respectively.

[willbrown]

Thank you.