User:Karmella Haynes/Notebook/PcTF Genomics/2014/02/10: Difference between revisions
From OpenWetWare
Line 18: | Line 18: | ||
* Paper reference for STAR is Lefterova MI, et al. Cell-specific determinants of peroxisome proliferator-activated receptor gamma function in adipocytes and macrophages. Mol Cell Biol. 2010;30(9):2078–2089. | * Paper reference for STAR is Lefterova MI, et al. Cell-specific determinants of peroxisome proliferator-activated receptor gamma function in adipocytes and macrophages. Mol Cell Biol. 2010;30(9):2078–2089. | ||
* Website for STAR is http://www.cbil.upenn.edu/STAR/ | * Website for STAR is http://www.cbil.upenn.edu/STAR/ | ||
* Bramswig et al. used the following setting in their STAR analysis: sliding window of 5, | * Bramswig et al. used the following setting in their STAR analysis: sliding window of 5,000 bp, step size of 1,000 bp, and a FDR=0.5%. | ||
PROCEDURE | PROCEDURE | ||
Line 41: | Line 42: | ||
| <extension length> || total fragment length minus the read length || 10 | | <extension length> || total fragment length minus the read length || 10 | ||
|- | |- | ||
| <start coordinate infile> || | | <start coordinate infile> || 0 or 1 depending on the whether the first position in each chromosome is denoted by 0 or 1 || 1 | ||
|- | |- | ||
| <right-end-inclusion infile> || ??? || true | | <right-end-inclusion infile> || ??? || true | ||
Line 49: | Line 50: | ||
| <numperms> || ??? || 10 | | <numperms> || ??? || 10 | ||
|- | |- | ||
| <remove identical reads> || | | <remove identical reads> || is 'false' if no, 'true' if yes || true | ||
|- | |- | ||
| <sample file> || ??? || test_data1.txt | | <sample file> || ??? || test_data1.txt | ||
|- | |- | ||
| <control> || | | <control> || 1) 'false', or 2) the name of the control file, or 3) the name of a file of regions to mask, in this case the name of the file must end in '_mask' || false | ||
|- | |- | ||
| <repeats file> || | | <repeats file> || 'false' if you don't want to mask repeats, otherwise is the name of a file of repeats with (tab delimited) format: chr start end (download here: cbil.upenn.edu/STAR/repeats) || false | ||
|- | |- | ||
| <output file name> || ??? || test_out | | <output file name> || ??? || test_out | ||
|- | |||
| <start coordinate outfile> || ??? || 1 | |||
|- | |||
| <right-end-inclusion outfile> || ??? || true | |||
|- | |||
| <window size> || ??? || 10 | |||
|- | |||
| <window displacement> || ??? || 5 | |||
|- | |||
| <normalize to this many reads> || ??? || 0 | |||
|} | |} | ||
Revision as of 15:24, 10 February 2014
Pc-TF Genomics | <html><img src="/images/9/94/Report.png" border="0" /></html> Main project page <html><img src="/images/c/c3/Resultset_previous.png" border="0" /></html>Previous entry<html> </html>Next entry<html><img src="/images/5/5c/Resultset_next.png" border="0" /></html> | ||||||||||||||||||||||||||||||||||||||||||||||||
02/10/14
ChIP-seq analysis via STAR
|