itmat rum issues - Githubissues

itmat / rum

RNA-Seq Unified Mapper

http://cbil.upenn.edu/RUM

MIT License

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issues

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Undefined subroutine &RUM::Script::Indexes::isdigit

#190 rashidma opened 2 years ago
2
Reads naming

#189 OlgaVT closed 4 years ago
2
RUM and Bowtie2

#188 katharinedickson opened 5 years ago
2
rum_runner says it uses a default --prefix, but it doesn't

#187 amirkarger opened 8 years ago
0
make test fails on several files due to "unsorted output"

#186 amirkarger opened 8 years ago
0
Test failed: merge-gnu-and-tnu-and-cnu.t & rum-to-sam.t

#185 hwlim opened 9 years ago
1
Test failed: merge-gnu-and-tnu-and-cnu.t & rum-to-sam.t

#184 hwlim opened 9 years ago
0
Unbundle mdust, blat and bowtie from the package

#183 mmokrejs opened 10 years ago
0
rum-2.0.5_05: Warning: the following files are missing in your kit: lib/RUM/Script/QuantifyExons.pm

#182 mmokrejs opened 10 years ago
1
Corrupt line from RUM_NU

#181 audreymannion opened 10 years ago
0
Proper sam formating

#180 choishingwan opened 10 years ago
2
Update Local.pm

#179 earonesty opened 10 years ago
0
LSF cluster

#178 khayer opened 10 years ago
2
Novel and known introns with same coordinates

#177 ryanames opened 10 years ago
0
Error creating index from ensembl gtf and genome

#176 mdelaurentis closed 11 years ago
0
Can't Generate plan for postprocessing.

#175 gotte opened 11 years ago
6
Cycle in chromosome comparison

#174 mdelaurentis closed 11 years ago
0
Don't use SAM file produced by the junction script

#173 mdelaurentis closed 11 years ago
0
Make sure the master branch is the current release

#172 delagoya closed 11 years ago
0
MAPQ should be set to "0" for unmapped reads in SAM file

#171 delagoya closed 11 years ago
4
junction score with paired-end data - is it # of reads or fragments?

#170 nmanik opened 11 years ago
4
Can't locate object method "newdir" via package "File::Temp"

#169 karinschlangen closed 11 years ago
5
Bug in calculation of IH:i in the SAM file?

#168 mdelaurentis opened 11 years ago
0
RUM and multiple hits

#167 snandy3 closed 11 years ago
2
Incorrect counts in mapping_stats file

#166 mdelaurentis opened 11 years ago
0
Mapping stats contains some junk

#165 mdelaurentis closed 11 years ago
0
trascriptomes

#164 safisher opened 11 years ago
0
SAM headers should be changed to contain all chromosomes

#163 mdelaurentis opened 11 years ago
0
RUM doesn't know it stopped

#162 asowalsky opened 11 years ago
11
another broken RUM job

#161 safisher opened 11 years ago
2
error during aligning

#160 safisher opened 11 years ago
0
Can't create new indices

#159 tianyang-li opened 11 years ago
7
multi-mapper in RUM_Unique... revisited

#158 safisher opened 11 years ago
2
Bowtie flags

#157 safisher opened 11 years ago
1
about custom index

#156 jlduan opened 11 years ago
1
Erroneous RUM_NU chunk

#155 safisher closed 11 years ago
2
Galaxy Support

#154 delagoya opened 11 years ago
2
Possible naming conflict with sort_RUM_by_location temp files

#153 mdelaurentis closed 11 years ago
1
Out of memory error?

#152 mdelaurentis closed 11 years ago
0
Name mapping file for FASTA input has blank lines

#151 mdelaurentis opened 11 years ago
0
--preserve-names not working?

#150 mdelaurentis closed 11 years ago
0
chunk sizes hugely off with *.gz input

#149 nmanik opened 11 years ago
4
RUM mistakenly flagging some fastq inpu as variable length

#148 mdelaurentis closed 11 years ago
0
sam format - TLEN field

#147 khayer closed 11 years ago
0
unmapped reads in sam file

#146 e-manduchi closed 11 years ago
5
quals.fa and quality scores

#145 nmanik opened 11 years ago
1
Document abbreviated options

#144 nmanik opened 11 years ago
4
user-specified qsub options

#143 nmanik closed 11 years ago
1
make test question

#142 nmanik closed 11 years ago
2
question on output file

#141 e-manduchi opened 11 years ago
5