Input File(s) Originals | Processing program | Output file(s) |
---|---|---|
./cDNA/allcdna.cdi | Probably | from GenBank flat files or via Entrez browser |
./features/sanger/syn | Obtained | possibly from Lincoln Stein |
./features/celegans.syn | Obtained | possibly from Lincoln Stein |
./nt4/*.dna.gz | fatont4 | ./nt4/*.nt4 |
./cDNA/allcdna.fa | indexfa | ./cDNA/allcdna.ix |
./?/*.gff | geniegff | ./features/sanger/c2g ./features/sanger/genes.gdf |
./genie/*.gff | geniegff | ./features/genie/c2g ./features/genie/genes.gdf |
./features/c2c | makepgo | ./features/*.coo |
./cDNA/allcdna.ix | refiAli | ./ga/good.txt ./ra/bad.txt ./ra/cool.txt |
./ga/good.txt | binGood | ./cDNA/good.ali |
./cDNA/good.ali | ali2alx | ./cDNA/*.alx |
./ra/good.txt | cdnaOff | ./cDNA/*.cdo> |
./ra/good.txt | introns | cDNA/introns.gff cDNA/introns.txt obsolete/altintron.txt $(html_root)/intronerator/altsplice.raw.html cDNA/introns.fa |
./cDNA/good.ali | ixali | ./cDNA/good.ix |
./ra/good.txt $(html_root)/intronerator/nameless.raw.html | cluster | ./features/c2g |
./features/c2g | ixword3 | ./features/c2g.ix |
./features/c2c | ixword3 | ./features/c2c.ix |
./features/sanger/genes.gdf | indexgl | ./features/sanger/genes.ix |
./features/c2g | makepgo | ./features/sanger/*.pgo |
./features/sanger/genes.gdf | indexgl | ./features/sanger/genes.ix |
./features/c2c | makepgo | ./features/*.coo |
./features/genie/c2g | makepgo | ./features/genie/*.pgo |
./features/sanger/syn ./features/syn | moresyn | ./features/orf2gene ./features/orfInfo |
./xeno/cbriggsae/all.st | ixxenost | ./xeno/cbriggsae/all.ix |
./xeno/cbriggsae/all.st | stToXao | ./xeno/cbriggsae/*.xao |
./makefile - looks like most files here are created by processes specified in this makefile ./README - brief listing of several files in cDNA, ra/good.txt and xeno/cbriggsae/all.st ./makefile.bak - garbage ./ea/all.zip - compressed all.out file - results of alignments ./nt4/i.nt4 - Are these 2-bit-a-base representations of DNA from lib/nt4.c ? ./nt4/ii.nt4 - by processing the dna.gz files below ? ./nt4/iii.nt4 ./nt4/iv.nt4 ./nt4/m.nt4 ./nt4/v.nt4 ./nt4/x.nt4 ./nt4/I.dna.gz - these dna.gz are the C. elegans chromosomes ./nt4/II.dna.gz ./nt4/III.dna.gz - This nt4 directory is an argument to refiAli in the makefile ./nt4/IV.dna.gz - which specifies chromDir ./nt4/M.dna.gz ./nt4/V.dna.gz ./nt4/X.dna.gz ./cDNA/ - I assume this directory is the C. elegans data ./cDNA/allcdna.ix - the .ix files are indexes to the .fa files ./cDNA/allcdna.fa - created by indexfa ./cDNA/introns.fa - list of introns in fa format, created by introns ./cDNA/good.ix ./cDNA/good.ali - a binary version of ga/good.txt created by binGood ./cDNA/i.alx - .alx index files created from good.ali via the ali2alx program ./cDNA/i.cdo - .cdo - cDNA offsets created from ra/good.txt via cdnaOff program ./cDNA/ii.alx ./cDNA/ii.cdo - cdnaOff creates an index for each chromosome from ra/good.txt ./cDNA/iii.alx - ali2alx creates an index for each chromsome from good.ali ./cDNA/iii.cdo ./cDNA/introns.gff - the intron feature file listing, see also GFF_Spec - created by introns ./cDNA/introns.txt - list of introns in GFF format, created by introns ./cDNA/iv.alx ./cDNA/iv.cdo ./cDNA/m.alx ./cDNA/m.cdo ./cDNA/v.alx ./cDNA/v.cdo ./cDNA/x.alx ./cDNA/x.cdo ./cDNA/allcdna.cdi - looks like these are from genBank to cDNA info file format via gb2cdi, see gb2cdi.c for field format ./ra/good.txt - each and every cDNA alignment described - the output of a run of refiAli (refineAli.c) ./ra/bad.txt.gz - from the output of refiAli, scores too low ./ra/cool.txt.gz - from the output of refiAli, unusual features ./ra/err.txt.gz ./features/c2c - looks like a list of identified features in sorted order by their coordinates ./features/c2c.ix - created by ixword3 from c2c ./features/i.coo - from makepgo run on c2c file - predicted gene offset files ./features/ii.coo - I can't find the difference between .coo and .pgo ./features/iii.coo ./features/iv.coo ./features/m.coo ./features/v.coo ./features/x.coo ./features/c2g - A cluster listing from sanger/c2g and ra/good.txt, from the output of cluster ./features/c2g.ix - created by ixword3 from c2g ./features/celegans.syn - A synonyms table, from where ? ./features/syn - Synonyms table ./features/orfInfo - info of ORFs, created by moresyn from the syn table ./features/orf2gene - orf to gene table, created by moresyn from syn table ./features/sanger/c2g - feature list from the sanger viewpoint ? ./features/sanger/genes.gdf - Genie gene predictions, From Sanger ? ./features/sanger/genes.ix - created by indexgl from genes.gdf ./features/sanger/i.pgo - predicted Gene Offset - from makepgo working on c2g ./features/sanger/ii.pgo ./features/sanger/iii.pgo ./features/sanger/iv.pgo ./features/sanger/v.pgo ./features/sanger/x.pgo ./features/sanger/m.pgo ./features/sanger/syn - A synonyms table, from Sanger ? ./features/genie/genes.gdf - Genie gene predictions, from genie/*.gff ./features/genie/c2g - a cluster listing, from what features ? ./features/genie/i.pgo - predicted gene offset files, via makepgo working on c2g ./features/genie/ii.pgo ./features/genie/iii.pgo ./features/genie/iv.pgo ./features/genie/v.pgo ./features/genie/x.pgo ./features/genie/m.pgo ./features/genie/genes.ix - from indexgl operating on genes.gdf ./genie/I.gff - The chromosomes feature files, defines CDS, what is CDS ? ./genie/II.gff - This says CDS is a cDNA ? ./genie/III.gff ./genie/makefile ./genie/IV.gff ./genie/V.gff ./genie/X.gff ./xeno/cbriggsae/all.st - cross species alignment file short stitched, from what ? filtRep.c maybe ? What data ? ./xeno/cbriggsae/all.ix - index created by ixxenost from all.st ./xeno/cbriggsae/i.xao - index files from all.st ./xeno/cbriggsae/ii.xao ./xeno/cbriggsae/iii.xao ./xeno/cbriggsae/iv.xao ./xeno/cbriggsae/v.xao ./xeno/cbriggsae/x.xao ./xeno/cbriggsae/m.xao ./foo - temporary shell file garbage ./trash/ - 29 Mb of trash, perhaps temp files used by the browser ?