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BBMap and BBmerge insert sizs

Hi all

Using bbmerge, we have insert size 161 and using bbmap we have insert size 182. Here is my commands :

./bbmap.sh -Xmx24g in1=pair1.fastq.gz in2=pair2.fastq.gz ihist=hist_map.txt reads=400000 ref=genome.fa

./bbmerge.sh in1= in1=pair1.fastq.gz in2=pair2.fastq.gz ihist=hist_merge.txt reads=400000 prefilter=2 rem extend2=100

Which one I should go for? Also what is the count in hist.txt, the sum of counts is higher than the number of reads.

rna-seq insert size
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updated by GenoMax GenoMax • written by Sharon Sharon

1 answer

If you are able to map then the bbmap.sh size is more accurate since you have truth available via reference. With bbmerge command you are using you are doing some k-mer based extension of the reads, so keep that in mind. What do you get if you remove prefilter=2 rem extend2=100?

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written by GenoMax GenoMax

If I still use reads=400000 and removed prefilter=2 rem extend2=100 I got 160 insert size.

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written by Sharon Sharon

Use the one from bbmap alignments.

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written by GenoMax GenoMax

So if the insert size is 180, then 2 *150 reads are overlapping wih 120 right? This is still short insert size, right? 

Insert size – 2 r = innermate 
180 -300 = -120 , right?
• 0 views • link
written by Sharon Sharon

Yes. While the inserts are relatively short that is a characteristic of this library. It will have to be remade, if longer inserts are desired.

|------------------------------->30 bp|    R1 - 150 bp
|-------------------------------------|    Fragment 180 bp
|30 bp<-------------------------------|    R2 - 150 bp
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written by GenoMax GenoMax

Thanks so much genomax

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written by Sharon Sharon

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