[smehr12]

You should draw the distribution.

Hi Ih3 ,
By distribution, you meant the library size distribution? or the reads that matched the subject?

[Jon_Keats]

For the Mate-Pair data you can reverse complement with the FastX package and then run as a standard PE run but with much larger inserts. Works fine unless you have a ton of reads crossing the circularized junction.

[mcgreevy]

error - weird pairing

Just thought I'd post this for posterities sake. I was getting the infer insert size -- weird pairing error but it was because the perl script i was running to call bwa was using the same fastq file for both sides of the pair end reads instead of using the two seperate files. perhaps this will save someone some trouble.

[Warr]

Just thought I'd post this for posterities sake. I was getting the infer insert size -- weird pairing error but it was because the perl script i was running to call bwa was using the same fastq file for both sides of the pair end reads instead of using the two seperate files. perhaps this will save someone some trouble.

Thank you for posting this, mcgreevy, you certainly saved me some trouble. I had a typo in my shell script .