What are the definitions of the BBMerge outinsert table file?
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3.0 years ago
Tawny ▴ 180

I have the output from the outinsert parameter of bbmerge.
I have been unable to find the explanation of the columns. Can someone explain the columns a bit more? There are status flags of I, P, or F. What do these mean? Here is an example of my file:

#id     numericID       insert  status  mismatches
M06940:10:000000000-JDD2F:1:1102:10778:1042 1:N:0:6     0       199     I       7
M06940:10:000000000-JDD2F:1:1102:10644:1042 1:N:0:6     1       -1      F
M06940:10:000000000-JDD2F:1:1102:12055:1043 1:N:0:6     2       -1      F
M06940:10:000000000-JDD2F:1:1102:14852:1043 1:N:0:6     3       -1      F
M06940:10:000000000-JDD2F:1:1102:15574:1045 1:N:0:6     4       -1      F
M06940:10:000000000-JDD2F:1:1102:14306:1046 1:N:0:6     5       -1      F
M06940:10:000000000-JDD2F:1:1102:14951:1046 1:N:0:6     6       -1      F
M06940:10:000000000-JDD2F:1:1102:12089:1046 1:N:0:6     7       -1      F
M06940:10:000000000-JDD2F:1:1102:12999:1046 1:N:0:6     8       196     I       1
M06940:10:000000000-JDD2F:1:1102:12750:1047 1:N:0:6     9       -1      F
M06940:10:000000000-JDD2F:1:1102:11670:1047 1:N:0:6     10      -1      F
M06940:10:000000000-JDD2F:1:1102:13751:1047 1:N:0:6     11      -1      F
M06940:10:000000000-JDD2F:1:1102:9753:1048 1:N:0:6      12      -1      F
M06940:10:000000000-JDD2F:1:1102:13621:1049 1:N:0:6     13      135     I       1
M06940:10:000000000-JDD2F:1:1102:13057:1050 1:N:0:6     14      158     I       2
M06940:10:000000000-JDD2F:1:1102:14929:1050 1:N:0:6     15      -1      F
M06940:10:000000000-JDD2F:1:1102:9442:1051 1:N:0:6      16      147     P       0
bbmerge outinsert • 732 views
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Did you ever find any information about this?

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No I never got a real answer to this. I am guessing that 'I' means it is Insert data, 'F' means there was no insert (Fail) and 'P' means Pass? But those are just guesses.

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Thanks. I had a look in the source code. Java is admittedly not a language I'm good with, but I believe that you're pretty close. P = Perfect, F=Failed, and I=Imperfect.

In my case, I added up the number of reads that had a "P" or "I" status, and it matched the total number of merged reads.

Curiously, I set the flag pfilter=1 to attempt to force only perfect matches to be retained, but a very small number of non-perfect matches made it into the merged results. I'm not certain why.


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