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dieterich-lab / JACUSA2

New version of JACUSA -> 2.0
GNU General Public License v3.0
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RefBase / ReadBase mismatch #11

Closed CDieterich closed 6 years ago

CDieterich commented 6 years ago

Hi Michael, in JACUSA_v2.0.0-S-BETA-1.jar

I still get this Refbase <=> ReadBase Mismatch

JACUSA Version: 2.0.0-S-BETA-1 rt-arrest -s -c 5 -p 10 -F 1024 -a S,I,M -P1 FR-FIRSTSTRAND -P2 FR-FIRSTSTRAND -S -R /biodb/genomes/mus_musculus/GRCm38_90/GRCm38_90.fa -r JACUSA2_RNA_KO_rt_arrest K002000225_86972_STARmapping_uniq_rmdup.bam,K002000225_86975_STARmapping_uniq_rmdup.bam,K002000225_86976_STARmapping_uniq_rmdup.bam K002000225_86971_STARmapping_uniq_rmdup.bam,K002000225_86974_STARmapping_uniq_rmdup.bam,K002000225_86973_STARmapping_uniq_rmdup.bam

results in /scratch/cdieterich/Claudia_BadNauheim/longRNA/workflow/JACUSA/

CDieterich commented 6 years ago

Ok, this problem only occurs for rows on the minus strand.

CDieterich commented 6 years ago

superceded