Just looking for a bit of advice.
I have concatenated forward read and concatenated reverse paired end read files for input into SOAPtrans de novo. I have been using Trinity to date and have been unaware of the insert size setting which comes with SOAP config file.
I have a few questions:
Using the concatenated read files (previously cleaned using Trimmomatic), I obtained an average insert size of 124bp (123.56bp) with the BBtools script BBmerge ( as outlined http://seqanswers.com/forums/showthread.php?t=43906 ) for my Illumina Hiseq 2500 data. Is this a normal insert size? I think Truseq chemistry kit was used.
Secondly, just to check with people that have more experience than myself;I am assuming it doesn't matter if all my forward reads are joined together for this calculating the insert size? I read about overlapping of reads. Having concatenated all my Fwd / Rev reads, surely this won't have any affect or cause an erroneous insert size reporting?
Thirdly, for SOAPtrans, the map_len (map length) is set to 32 default. Whilst I have changed the other settings to suit my insert size (124bp), and max read size of 88 (trimmed from 100bp in trimmomatic), should I also be changing map length?