PairedreadFinder or similar?

[kga1978]

Hi,

I have two fastq files that originated from a matched paired-end library (mate-pair1.fastq and mate-pair2.fastq), but I have now trimmed them and they contain different numbers of reads and are out of sync. Some of the reads have matched pairs, but others don't. Is there a program that can fix this for me? I know 'PairedreadFinder' (part of earlier versions of FAR) can do this, but I can't get this program to work (keep getting 'error while loading shared libraries: libtbb.so.2' even though I copied the required library to the same folder as FAR/PairedreadFinder). I know of a few perl scripts out there but they require a ton of memory and aren't very efficient.

Any help would be greatly appreciated.

[sklages]

adjust you LD_LIBRARY_PATH to point to the directory containing the library; then the program should work (or give you another error message) ..

[nsl]

Not sure whether you fixed the problem, but I think you can you can use "Filter SAM" under "SAM TOOLs" in galaxy as an alternative.