Merge branch 'master' of git.biohpc.swmed.edu:BICF/Astrocyte/process_scripts

alignment/rnaseqalign.sh

@@ -70,8 +70,6 @@ else
 	samtools view -1 --threads $SLURM_CPUS_ON_NODE -o output.bam out.sam
     fi
     samtools sort -@ $SLURM_CPUS_ON_NODE -O BAM -o ${pair_id}.bam output.bam
-    java -jar $PICARD/picard.jar FixMateInformation ASSUME_SORTED=TRUE SORT_ORDER=coordinate ADD_MATE_CIGAR=TRUE I=output.nsort.bam O=${pair_id}.bam
-
 fi
 
 samtools index -@ $SLURM_CPUS_ON_NODE ${pair_id}.bam

alignment/starfusion.sh

@@ -49,7 +49,7 @@ then
 	mkdir $tmphome
     fi 
     export TMP_HOME=$tmphome
-    index_path=${refgeno}/CTAT_lib_trinity/
+    index_path=${refgeno}/CTAT_lib_trinity1.6
     trinity /usr/local/src/STAR-Fusion/STAR-Fusion --min_sum_frags 3 --CPU $SLURM_CPUS_ON_NODE --genome_lib_dir ${index_path} --left_fq ${fq1} --right_fq ${fq2} --examine_coding_effect --output_dir ${pair_id}_star_fusion
     #cp ${pair_id}_star_fusion/star-fusion.fusion_predictions.abridged.tsv ${pair_id}.starfusion.txt
     cp ${pair_id}_star_fusion/star-fusion.fusion_predictions.abridged.coding_effect.tsv ${pair_id}.starfusion.txt