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itmat / Normalization

RNA-Seq normalization and quantification pipeline
https://github.com/itmat/normalization/wiki
GNU General Public License v3.0
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un-necessary warning in runall_sam2junctions.pl #4

Open e-manduchi opened 10 years ago

e-manduchi commented 10 years ago

I've done my alignment with STAR. In the output log file for this script I have warnings such as: "Warning: chr 'PN:STAR' not in your genome sequence file." The problem traces back to the MakeRumJunctionFiles.pm, line 410. STAR alignments start with lines such as: "@PG ID:STAR PN:STAR VN:STAR_2.3.0e_r291 CL:/gpfs/fs121/apps/STAR/current/STAR --runThreadN 6 --genomeDir /g pfs/fs121/apps/STAR/current/indexes/Sscrofa10.2.73/ --genomeLoad LoadAndRemove --readFilesIn /gpfs/fs121/h/manduchi /HFHC_12-8w_20w/READS/P_20w/P_20w_1.fq /gpfs/fs121/h/manduchi/HFHC_12-8w_20w/READS/P_20w/P_20w_2.fq cl:/gpf s/fs121/apps/STAR/current/STAR --genomeDir /gpfs/fs121/apps/STAR/current/indexes/Sscrofa10.2.73/ --genomeLoad LoadAnd Remove --readFilesIn /gpfs/fs121/h/manduchi/HFHC_12-8w_20w/READS/P_20w/P_20w_1.fq /gpfs/fs121/h/manduchi/HFHC_12-8w_20w /READS/P_20w/P_20w_2.fq --runThreadN 6 "

this is where 'PN:STAR' is, this line is a comment line (@) and should be disregarded all together. I realize this is very minor and innocuous, but recording it as an issue in lack of better place to record this.