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21 Commits
README
README
 
 
all2many.pl
all2many.pl
 
 
bam2sam.sh
bam2sam.sh
 
 
bedlengths.pl
bedlengths.pl
 
 
bedmid.pl
bedmid.pl
 
 
bedtss.pl
bedtss.pl
 
 
blat.sh
blat.sh
 
 
breakfasta.pl
breakfasta.pl
 
 
checkservers.sh
checkservers.sh
 
 
chromsizeswin.pl
chromsizeswin.pl
 
 
colMeans.pl
colMeans.pl
 
 
colgrep.sh
colgrep.sh
 
 
collapse.pl
collapse.pl
 
 
collapse.sh
collapse.sh
 
 
colors.pl
colors.pl
 
 
colors.sh
colors.sh
 
 
concatfasta.pl
concatfasta.pl
 
 
countbam.sh
countbam.sh
 
 
cutmulti.sh
cutmulti.sh
 
 
deriv.pl
deriv.pl
 
 
double.pl
double.pl
 
 
fakeid.pl
fakeid.pl
 
 
fasta2pwm.pl
fasta2pwm.pl
 
 
fastaheaders.pl
fastaheaders.pl
 
 
fastq2flat.pl
fastq2flat.pl
 
 
fetchChromSizes.sh
fetchChromSizes.sh
 
 
filterbed.pl
filterbed.pl
 
 
findzeros.pl
findzeros.pl
 
 
fix.pl
fix.pl
 
 
fixcols.pl
fixcols.pl
 
 
flatten.pl
flatten.pl
 
 
flatten2.pl
flatten2.pl
 
 
flatten_ragged.pl
flatten_ragged.pl
 
 
fpkm2bed.pl
fpkm2bed.pl
 
 
gal_check.pl
gal_check.pl
 
 
gcfiltfasta.pl
gcfiltfasta.pl
 
 
gen_logos.pl
gen_logos.pl
 
 
get_chroms.R
get_chroms.R
 
 
interlace.pl
interlace.pl
 
 
introns_from_gtf.pl
introns_from_gtf.pl
 
 
keeplongestbed.pl
keeplongestbed.pl
 
 
lenfiltfasta.pl
lenfiltfasta.pl
 
 
lines.pl
lines.pl
 
 
make60.pl
make60.pl
 
 
makefasta.pl
makefasta.pl
 
 
makerandom.pl
makerandom.pl
 
 
makewin.pl
makewin.pl
 
 
modcol.pl
modcol.pl
 
 
mysplitter.pl
mysplitter.pl
 
 
parseBlast.pl
parseBlast.pl
 
 
parseBlat.pl
parseBlat.pl
 
 
parseInParanoid.pl
parseInParanoid.pl
 
 
parse_bowtie2_err.pl
parse_bowtie2_err.pl
 
 
parse_bowtie2_paired_err.pl
parse_bowtie2_paired_err.pl
 
 
parse_bowtie_err.pl
parse_bowtie_err.pl
 
 
parse_fastx_clipper_err.pl
parse_fastx_clipper_err.pl
 
 
partfasta.pl
partfasta.pl
 
 
password.php
password.php
 
 
random_bed.pl
random_bed.pl
 
 
random_beds.sh
random_beds.sh
 
 
random_beds_dir.sh
random_beds_dir.sh
 
 
randomlines.pl
randomlines.pl
 
 
range.sh
range.sh
 
 
rearrange.pl
rearrange.pl
 
 
remove_NA.pl
remove_NA.pl
 
 
remove_overlaps.pl
remove_overlaps.pl
 
 
remove_roman.pl
remove_roman.pl
 
 
remove_scinums.pl
remove_scinums.pl
 
 
renamebed.pl
renamebed.pl
 
 
renamefasta.pl
renamefasta.pl
 
 
renamefasta2.pl
renamefasta2.pl
 
 
resize.sh
resize.sh
 
 
revcompfasta.pl
revcompfasta.pl
 
 
revfasta.pl
revfasta.pl
 
 
revfastq.pl
revfastq.pl
 
 
selectlines.pl
selectlines.pl
 
 
sparsewig.pl
sparsewig.pl
 
 
split_bed.pl
split_bed.pl
 
 
split_by_col.pl
split_by_col.pl
 
 
split_wig.pl
split_wig.pl
 
 
squish.pl
squish.pl
 
 
strip_headers.sh
strip_headers.sh
 
 
subfasta.pl
subfasta.pl
 
 
substringfasta.pl
substringfasta.pl
 
 
sumbed.pl
sumbed.pl
 
 
thumbs.sh
thumbs.sh
 
 
tm.pl
tm.pl
 
 
tm_walk.pl
tm_walk.pl
 
 
translate_ids.pl
translate_ids.pl
 
 
truncbg.pl
truncbg.pl
 
 
truncwig.pl
truncwig.pl
 
 
uc.pl
uc.pl
 
 
ucscify.sh
ucscify.sh
 
 
undofasta.pl
undofasta.pl
 
 
uniq_fa.sh
uniq_fa.sh
 
 
uniq_gtf.pl
uniq_gtf.pl
 
 
uniq_vars.sh
uniq_vars.sh
 
 
uniqbed.pl
uniqbed.pl
 
 
uniqs.sh
uniqs.sh
 
 
vstep_to_bedgraph.pl
vstep_to_bedgraph.pl
 
 

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Tue May 17 13:12:09 CDT 2011

Here's a bunch of unpolished, possibly undocumented scripts of varying ages. May the world find them useful and not terribly terrible.

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A bunch of scripts for bioinformatic purposes

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