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25 Open 28 Closed
25 Open 28 Closed
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Issues list

Error align local mode_exit type 2
#88 opened Dec 3, 2018 by gianmaz
release new rail to include update to fastq-dump version
#87 opened Mar 15, 2018 by ChristopherWilks
Stuck at Step 4/24: Align reads and segment them into readlets
#85 opened Dec 13, 2017 by undiagnosed
4
Provide rse_gene and rse_exon tables in the rail output
#83 opened Nov 30, 2017 by yevishere
Supress intermediary bw option
#82 opened Nov 30, 2017 by yevishere
Allow --tag specification
#81 opened Nov 30, 2017 by BenLangmead
1
Spurious error about existing bucket
#75 opened Nov 29, 2017 by BenLangmead
Python subprocess OSError
#69 opened Nov 11, 2017 by symbiologist
address make_temp_dir(common) in emr_simulator
#49 opened Oct 1, 2016 by nellore
Normalize mean consistent with recount
#48 opened Sep 1, 2016 by lcolladotor
add precision/recall tests to line.py
#45 opened Jul 4, 2016 by nellore
make it obvious which log file has the error when dooplicity fails on a step in local/parallel modes
#43 opened Jun 28, 2016 by nellore
1
Unresolved ids in align_reads_delegate.py
#41 opened Jun 28, 2016 by BenLangmead
Making this work with bioconda?
#34 opened May 9, 2016 by DCGenomics
1
missing isofrags.tar.gz in parallel mode (v0.2.3b)
#33 opened Apr 18, 2016 by jfear
2
partition pipeline so high-utilization steps can use different instance type from low-utilization steps
#32 opened Feb 17, 2016 by BenLangmead
ideas for major feature additions in 0.3.0
#28 opened Jul 27, 2015 by nellore
do something about 255'd mapqs
#24 opened Apr 8, 2015 by nellore
add job flow resume feature
#20 opened Mar 27, 2015 by nellore
1
add uninstall
#18 opened Mar 23, 2015 by nellore
use ncbi/ngs library to slurp in SRA reads enhancement
#17 opened Mar 5, 2015 by BenLangmead
1
explore using lz4 rather than gzip in parallel/local modes
#16 opened Feb 27, 2015 by nellore
use latest gnu coreutils sort to increase speed in local/parallel mode; bundle with rail
#15 opened Feb 21, 2015 by nellore
add counters for debugging
#9 opened Oct 6, 2014 by nellore
1
address consistency of mapqs; check unique.h of bt2 to figure this out
#5 opened Aug 13, 2014 by nellore
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