BBMap output meaning

Question

[Tania]

Hi All 

Does anyone understand the following top lines from BBMap ihist output;
I use some previous biostars to run it but can't get what are the `#InsertSize` and `Count`.

Does it mean the first insert size is 77? Then can we have insert sizes = 1 as in the end of the output?

    Here is my output:
    #Mean   193.157
    #Median 168
    #Mode   145
    #STDev  396.478
    #PercentOfPairs 92.468
    #InsertSize     Count
    1       77
    2       87
    3       105
    4       107
    5       98
    6       92
    7       94
    8       103
    9       121
    10      112
   ..... .... ... .. 


    29754   1
    29919   1
    30005   1
    30062   1
    30481   1
    30732   1
    31142   1

[GenoMax]

Can you provide the full command line used?

[Tania]

I used the following command, found it somewhere in biostars:

 ./bbmap.sh -Xmx50g  in1=Sread1.fastq.gz in2=Sread2.fastq.gz ihist=histmap1m.txt reads=1000000 ref=human_genome.fa

[GenoMax]

I am not sure why you have insert sizes that small and with quite a few counts as well. Has this data been trimmed? You probably should have set a minlen=25 when you trimmed the data to avoid getting very short reads.

[Tania]

Sorry to bother again. But which column is the insert sizes? the count column? These are the raw data before doing anything.

[GenoMax]

#InsertSize     Count

First column should be insert size and second column is count of fragments with that insert size.

Have you scanned/trimmed this data? Can you try that?

I will tag @Brian Bushnell on this thread so he can offer his take. Please be aware that he has been busy of late and it may be a few days before he may look at this.

[Tania]

Edited: Thanks genomax, much appreciated ! I will use the trimmed data and see the difference. But this also mean we have too big insert sizes at end? Does this make sense?

[GenoMax]

Tagging: Brian Bushnell