Genomicus bedtools issues

Genomicus / bedtools

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-split flag doesn't work properly

#172 GoogleCodeExporter opened 9 years ago
0
shuffleBed with -incl and -chrom not keeping chromosome positions right

#171 GoogleCodeExporter opened 9 years ago
0
genomeCoverageBed produces non-standard bedgraph files whenever large coverage depth (more than 1000000) is encountered

#170 GoogleCodeExporter opened 9 years ago
0
BedTools multiinter doesn't determine intersecting coordinates in two files

#169 GoogleCodeExporter opened 9 years ago
0
slop produces garbage results with negative extension sizes

#168 GoogleCodeExporter opened 9 years ago
0
Unexpected overlap between adjacent (non-overlapping) features

#167 GoogleCodeExporter closed 9 years ago
3
Bed files overlap, but intersectBed reporting 0 overlaps

#166 GoogleCodeExporter opened 9 years ago
9
overlap reported with -wo does not honor -split

#165 GoogleCodeExporter opened 9 years ago
3
/lib64/libz.so.1: version `ZLIB_1.2.3.3' not found

#164 GoogleCodeExporter opened 9 years ago
0
increase window size

#163 GoogleCodeExporter opened 9 years ago
4
bamToBed error:"terminate called after throwing an instance of 'std::out_of_range'"

#162 GoogleCodeExporter opened 9 years ago
3
GenomeCoverage on non-numbered chromosomes

#161 GoogleCodeExporter opened 9 years ago
3
Invalid option in windowBed?

#160 GoogleCodeExporter opened 9 years ago
1
Installing BEDTool

#159 GoogleCodeExporter closed 9 years ago
2
bamtobed with split and tag options not working

#158 GoogleCodeExporter closed 9 years ago
1
pairtobed dies on RNA-seq bam

#157 GoogleCodeExporter opened 9 years ago
0
bamtools sort no longer working

#156 GoogleCodeExporter opened 9 years ago
0
allow output format to be explicitly set as .bed or .gtf for all commands

#155 GoogleCodeExporter opened 9 years ago
0
merge bed and intervals in which start=stop

#154 GoogleCodeExporter opened 9 years ago
1
Bedtools can not read tab delimited file

#153 GoogleCodeExporter opened 9 years ago
0
retain _1 & _2 strand information in bedpe

#152 GoogleCodeExporter opened 9 years ago
0
multibamcov not removing duplicates

#151 GoogleCodeExporter opened 9 years ago
0
intersectBed with bam will not write to file

#150 GoogleCodeExporter opened 9 years ago
1
ERROR "Start was greater than end" on [0,0) interval

#149 GoogleCodeExporter opened 9 years ago
0
make command not found

#148 GoogleCodeExporter opened 9 years ago
4
intersectBed -split does not work

#147 GoogleCodeExporter opened 9 years ago
3
intersectBed will not work with files sorted in the standard manner and -sorted option

#146 GoogleCodeExporter opened 9 years ago
10
closest command missing results

#145 GoogleCodeExporter closed 9 years ago
1
closestBed unexpected (lack of) output when missing nearest feature

#144 GoogleCodeExporter closed 9 years ago
3
bamToBed emits error if bam's RNAME is *

#143 GoogleCodeExporter opened 9 years ago
0
subtractbed error

#142 GoogleCodeExporter opened 9 years ago
3
intersect returns incorrect results when combined with -sorted option

#141 GoogleCodeExporter closed 9 years ago
2
Feature request: paired-end stranded RNA-seq .bam

#140 GoogleCodeExporter opened 9 years ago
0
bamToBed is not handling paired-end bam reads

#139 GoogleCodeExporter opened 9 years ago
3
-u for pairToPair

#138 GoogleCodeExporter opened 9 years ago
0
Warnings should go into STDERR, not STDOUT

#137 GoogleCodeExporter closed 9 years ago
1
closestBed returns more than one when the features overlapped.

#136 GoogleCodeExporter closed 9 years ago
2
intersectBed -wo -s reporting overlaps with different strands

#135 GoogleCodeExporter opened 9 years ago
3
bedtobam does not fail gracefully on bad input.

#134 GoogleCodeExporter opened 9 years ago
0
flank tool generates out of chromosome boundaries

#133 GoogleCodeExporter closed 9 years ago
3
Error with make

#132 GoogleCodeExporter opened 9 years ago
0
pairToBed return Bam reads with start or end base matching Bed intervals

#131 GoogleCodeExporter opened 9 years ago
1
Losing reads by BamToBed

#130 GoogleCodeExporter closed 9 years ago
2
BamToBed (bedpe) discards too many lines after unpaired reads

#129 GoogleCodeExporter closed 9 years ago
1
genomeCoverageBed raising input error

#128 GoogleCodeExporter closed 9 years ago
3
coverageBed from version 2.15 fails to prduce the correct depth of coverage if split option was selected

#127 GoogleCodeExporter closed 9 years ago
2
annotateBed and names options

#126 GoogleCodeExporter closed 9 years ago
3
intersectBed with a large bam file

#125 GoogleCodeExporter closed 9 years ago
5
GFF features with length 1 cannot be intersected

#124 GoogleCodeExporter closed 9 years ago
4
FastaFromBed error when a chr is not in the genome

#123 GoogleCodeExporter closed 9 years ago
3