Sort fastq files in order of quality?

[naragam]

Hi,

Does anybody have some util(s) to sort out very large (30G+) fastq files in order of quality numbers?

I also need some help in getting the lz library (lib32z1-dev) available to make the bioawk tool on my Ubuntu 64-bit PC running a 32-bit 12.04 LTS. For some reason the ld cannot resolve the lib32z1-dev even though it has been sudo-apt gotten and installed.

TiA, Nash

[GenoMax]

Hi,

I also need some help in getting the lz library (lib32z1-dev) available to make the bioawk tool on my Ubuntu 64-bit PC running a 32-bit 12.04 LTS. For some reason the ld cannot resolve the lib32z1-dev even though it has been sudo-apt gotten and installed.

TiA, Nash

Did you install the wrong library? Not sure what you mean by "64-bit PC running 32-bit OS"?

[naragam]

lz library install...

The h/w on my PC supports 64-bit OSes (not sure whether it's little or big endian) but the Ubuntu Linux that has been installed is 32-bit. I guess the reason for installing the lib32z1 is that libz is different for 32 and 64 bit OSes.
In any case, I don't understand why ld can't see the libz and it fails to make the bioawk tool.

Nash

[GenoMax]

The h/w on my PC supports 64-bit OSes (not sure whether it's little or big endian) but the Ubuntu Linux that has been installed is 32-bit. I guess the reason for installing the lib32z1 is that libz is different for 32 and 64 bit OSes.
In any case, I don't understand why ld can't see the libz and it fails to make the bioawk tool.

Nash

Have you tried appending the right path for libz to (or defining) $LD_LIBRARY_PATH?

[naragam]

libz problems

Have you tried appending the right path for libz to (or defining) $LD_LIBRARY_PATH?

Hmm....looks like it never installed libz...stupid me.... I can't find it on my system. The sudo apt-get actually fails saying that it cannot find the library. So, any idea how I can find the libz for my system? Most of the other apt-gets have worked magically so far....but this libz thingy seems tricky.

Nash

[arkal]

The h/w on my PC supports 64-bit OSes (not sure whether it's little or big endian) but the Ubuntu Linux that has been installed is 32-bit. I guess the reason for installing the lib32z1 is that libz is different for 32 and 64 bit OSes.
In any case, I don't understand why ld can't see the libz and it fails to make the bioawk tool.

Nash

Thats not an issue Just an example to suggest that the OS integer size doesn't matter is the fact that most windows users use 64 bit compatible hardwares but almost all windows versions before windows 7 are written in 32 bit architecture

[rmdavies]

Hmm....looks like it never installed libz...stupid me.... I can't find it on my system. The sudo apt-get actually fails saying that it cannot find the library. So, any idea how I can find the libz for my system? Most of the other apt-gets have worked magically so far....but this libz thingy seems tricky.

Nash

You need to install zlib1g-dev. That should give you zlib.h and libz.so so that you can compile and link against libz. Yes, the package is somewhat obscurely named.

The lib32z1 package is only needed if you are running 32 bit software on a 64 bit operating system. In your case, you are running a 32 bit O/S, so you already have the 32 bit version. This is why apt-get fails - lib32z1 is only included with the 64 bit distribution.

Rob.