Sentence examples for seq files from inspiring English sources

Rmps: the most probable sequence (MPS) of a read; this sequence is the one given in the seq files which are generally used by many aligners as the only input.

In general, "seq files" contained sequences of perfect readability covering over 300 400 nucleotides; in three cases, only 50 100 nucleotides could have beed read because of numerous "N" nucleotides (background noise).

Two aligners were chosen for comparing results: Eland: as the aligner of choice provided by Illumina, we used Eland as an example of aligners that align the MPSs of reads provided in the seq files.

The most probable identity of that base is called according to these probabilities resulting in a final read sequence which is reported in a seq file.

This allowed for comparing the analysis of the TF ChIP-seq files versus control ChIP-seq files.

We converted the downloaded the.csv ChIP-Seq files to.bed files and uploaded them to Genomatix GGA.

The RNA-Seq files were analyzed using the Lasergene Genomics Suite (DNASTAR , Inc Madison, USA).

Illumina RNA-Seq files for several species were downloaded from the NCBI Sequence Read Archive database (http://www.ncbi.nlm.nih.gov/sra/).nih.gov/sra/

Detailed information summarizing all the used ChIP-seq files is presented in Additional file 3: Table S1.

To facilitate analysis of this data set by others, all ChIP-seq files used here have been deposited in ArrayExpress under a single accession number E-MTAB-1509 E-MTAB-1509 E-MTAB-1509

ChIP-seq and RNA-seq files were converted to the bigwig format, then uploaded as custom tracks to the UCSC genome browser [ 69].