MWSchmid / filterReads

a tool to filter NGS reads

filterReads

I am currently working on a (rather simple) program that filters short reads using a set of defined sequences which shall be ignored (the motivation behind this was the observation that some RNA-Seq samples have an obscene number of reads aligning to ribosomal DNA - which messes up Rcount-multireads as it results in a huge RAM requirement for the multireads). I uploaded an early version. The filter based on sequences seems to work. The other filters are not tested yet. Note that one requires the qtiocompressor to compile it (more info in future or on request). I recommend running this version in any case from the command line (to see what happens in the background if you are using the GUI).

Binary for Ubuntu-like linux

Note: it assumes PHRED quality scores with an offset of 33 (inline documentation and messaging was wrong before). That's Sanger and Illumina 1.8+ format (details on wikipedia). Data on SRA is generally encoded like this. It's fixed in the Qt5 binary (which is untested though):

Binary for Ubuntu-like linux (Qt5, untested)

To start a GUI:

./p502filterReads

To run on command-line:

./p502filterReads -c arguments
# check the arguments with
./p502filterReads --help

You may also need to copy the iocompressor libraries

sudo cp /path/to/filterReads/qtiocompressor-2.3_1-opensource/lib/libQtSolutions_IOCompressor-2.3.so.1.0.0 /usr/local/lib/
sudo ln -s /usr/local/lib/libQtSolutions_IOCompressor-2.3.so.1.0.0 /usr/local/lib/libQtSolutions_IOCompressor-2.3.so
sudo ln -s /usr/local/lib/libQtSolutions_IOCompressor-2.3.so.1.0.0 /usr/local/lib/libQtSolutions_IOCompressor-2.3.so.1
sudo ln -s /usr/local/lib/libQtSolutions_IOCompressor-2.3.so.1.0.0 /usr/local/lib/libQtSolutions_IOCompressor-2.3.so.1.0
# that may be needed as well:
export LD_LIBRARY_PATH="/usr/local/lib"