Update fatbody hemocyte mapping commands.txt

Figure 2,3,S2,S3 - RNA-seq/fatbody hemocyte mapping commands.txt

@@ -1,5 +1,3 @@
-fatbody
-
 /scratch/Arun/Projects/example/STAR-2.6.0a/source/STAR --runMode genomeGenerate --genomeDir STARindex/ --genomeFastaFiles dmel-all-chromosome-r6.28.fasta --sjdbGTFfile dmel-all-r6.28.gtf --sjdbOverhang 49 --runThreadN 20&
 
 for file in *3.r_1.fq.gz; do java -jar /scratch/Arun/Software/Trimmomatic-0.36/trimmomatic-0.36.jar SE -phred33 $file ${file/3.r_1.fq.gz/3.r_trim_1.fq.gz} ILLUMINACLIP:/scratch/Arun/Software/Trimmomatic-0.36/adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 -threads 25; done&
@@ -19,4 +17,4 @@ java -Xmx4G -jar /scratch/Arun/Projects/example/QoRTs.jar --singleEnded –maxRe
 for file in *.s_3.r_trim_1.fq.gz; do /scratch/Arun/Projects/example/STAR-2.6.0a/source/STAR --runMode alignReads --genomeDir /scratch/Arun/Reference/Drosophila_melanogaster/Flybase/STARindex/ --readFilesIn $file --readFilesCommand zcat --outFileNamePrefix ${file/.s_3.r_trim_1.fq.gz/rRNA/} --outFilterMultimapNmax 10000000000 --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --twopassMode Basic --runThreadN 35; done&
 
 
-/scratch/Arun/Projects/example/subread-1.6.2-source/bin/featureCounts -t gene -a /scratch/Arun/Reference/Drosophila_melanogaster/Flybase/dmel-all-r6.28.gtf -Q 10 -o gene_count_mq10.txt -T 15 *.out.bam >out 2>err&
+/scratch/Arun/Projects/example/subread-1.6.2-source/bin/featureCounts -t gene -a /scratch/Arun/Reference/Drosophila_melanogaster/Flybase/dmel-all-r6.28.gtf -Q 10 -o gene_count_mq10.txt -T 15 *.out.bam >out 2>err&