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"SAM\n\nA SAM file (.sam) is a tab-delimited text file that contains sequence alignment data. A BAM file (.bam) is the binary version of a SAM file. These formats are described on the SAM Tools web site: http://samtools.sourceforge.net.\n\nIndexing: IGV requires that both SAM and BAM files be sorted by position and indexed, and that the index files follow a specific naming convention. Specifically, a BAM index file should be named by appending ".bai" to the bam file name. A SAM index filename is created by appending ".sai". In both cases the index files must reside in the same directory as the BAM or SAM file. \n\nTools for sorting and indexing BAM files are available at the SAM Tools website referenced above. SAM files can be sorted and indexed using the igvtools package. \n\nChromosome names: Chromosome names must be consistent across all annotation and data files. For convenience, IGV equates chromosome numbers and names of the form chr# (e.g. 1 and chr1 are equivalent).\n\nOne-based index: Start and end positions are identified using a one-based index. The end position is included. For example, setting start-end to 1-2 describes two bases, the first and second in the sequence."

Yet another cloud file transfer service

How do I setup NFS v4.0 distributed file system access server under CentOS / RHEL v5.x for sharing files with UNIX and Linux workstations? How to export a directory with NFSv4? How to mount a directory with NFSv4?

"Expression Console™ software supports probe set summarization and CHP file generation for 3' expression (e.g., GeneChip® Human Genome U133 Plus 2.0 Array), gene-level (e.g., GeneChip® Human Gene 1.0 ST array) and exon-level arrays (e.g., GeneChip® Human Exon 1.0 ST Array). The Expression Console workflow provides the user with a choice of the more commonly used probe set summarization algorithms. The algorithms offered include: * MAS5 Statistical algorithm * Probe Logarithmic Intensity Error Estimation (PLIER) * Robust Multichip Analysis (RMA)"

"TMHMM Server v. 2.0\nPrediction of transmembrane helices in proteins\n\nNOTE: You can submit many proteins at once in one fasta file. Please limit each submission to at most 4000 proteins. Please tick the 'One line per protein' option. Please leave time between each large submission. "

Phred\n\nThe phred software reads DNA sequencing trace files, calls bases, and assigns a quality value to each called base.