Tophat aligner v2.0.10 (as well as earlier versions) fails to process FASTQ reads in color space:
$ tophat2 --color --bowtie1 E_coli_k12.ASM584v1.14.dna.chromosome.Chromosome color.fastq [2014-02-02 18:53:18] Beginning TopHat run (v2.0.10) ----------------------------------------------- [2014-02-02 18:53:18] Checking for Bowtie Bowtie version: 188.8.131.52 [2014-02-02 18:53:18] Checking for Samtools Samtools version: 0.1.19.0 [2014-02-02 18:53:18] Checking for Bowtie index files (genome).. [2014-02-02 18:53:18] Checking for reference FASTA file [2014-02-02 18:53:18] Generating SAM header for E_coli_k12.ASM584v1.14.dna.chromosome.Chromosome [2014-02-02 18:53:19] Preparing reads left reads: min. length=50, max. length=50, 1 kept reads (0 discarded) [2014-02-02 18:53:19] Mapping left_kept_reads to genome E_coli_k12.ASM584v1.14.dna.chromosome.Chromosome with Bowtie [FAILED] Error running bowtie: Too few quality values for read: 1T3/ are you sure this is a FASTQ-int file? libc++abi.dylib: terminate called throwing an exception
Here is a patch. (What to do with it: save it to the directory containing Tophat sources "tophat-2.0.10", run "patch -p0 < bam2fastx.cpp.patch", and rebuild Tophat.)
(Reads in FASTA+qual format are processed correctly, so if you need just to align some FASTQ file, you can convert it to FASTA+qual with some converter, such as QIIME or "read_fastq -i input.fastq | write_454 -o input.fasta -q input.qual -x" from biopieces.org).
If you use a pattern fill in your xfig drawing, and then convert it to PostScript or PDF, you'll find that the resulting file has embedded type 3 fonts. Type 3 is almost never accepted nowadays at most places where you want to submit your paper. Recompile transfig (the software coming with xfig, which converts .fig drawings to various formats) with these patches, and you'll not be getting the unexpected bitmapped fonts in your pdf any more.
For transfig v.3.2.5-alpha5: included in patchlevel 5-alpha6 (available from xfig download page).
For transfig v.3.2.4 (last stable version at the moment of this writing): transfig.3.2.4.patch.diff.gz.