Update RNA_base_processing.sh

loosolab · Apr 14, 2023 · 9bc1aab · 9bc1aab
1 parent 73e5a94
commit 9bc1aab
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/RNA/RNA_base_processing.sh b/RNA/RNA_base_processing.sh
@@ -20,10 +20,10 @@ java -jar trimmomatic.jar SE -threads 8 ./raw/${sample_prefix}_R1.fastq ./trim/$
 STAR --genomeDir /mnt/flatfiles/organisms/new_organism/mus_musculus/101/index_star --runThreadN 16 --readFilesIn ./trim/${sample_prefix}_R1_trim.fastq --outReadsUnmapped Fastx --outFileNamePrefix ./star/${sample_prefix} --outSAMstrandField intronMotif --outSAMtype BAM Unsorted --genomeLoad LoadAndKeep --outFilterMismatchNoverLmax 0.1 --outFilterMatchNmin 20 --alignIntronMax 200000 --alignMatesGapMax 2000 --alignEndsProtrude 10 ConcordantPair --outMultimapperOrder Random --limitOutSAMoneReadBytes 10000000 --sjdbOverhang 100 --outFilterMultimapNmax 1
 
 ## Generate BigWig normalized to mapped reads per sample: python package deeptools 3.5.1 / bamCoverage
-bamCoverage -b ./star/${sample_prefix}_nodup_filter.bam -o ./star/${sample_prefix}_nodup_filter.bw -p 16 --binSize 25 --smoothLength 75 --normalizeUsing RPKM --outFileFormat bigwig
+bamCoverage -b ./star/${sample_prefix}.bam -o ./star/${sample_prefix}.bw -p 16 --binSize 25 --smoothLength 75 --normalizeUsing RPKM --outFileFormat bigwig
 
 ## Count reads per genes: subread featureCounts
-featureCounts -T 16 -o ./star/${sample_prefix}_fcounts.txt -t exon -g gene_id -s 1 -a mus_musculus.101.mainChr.gtf ./star/${sample_prefix}_nodup_filter.bam
+featureCounts -T 16 -o ./star/${sample_prefix}_fcounts.txt -t exon -g gene_id -s 1 -a mus_musculus.101.mainChr.gtf ./star/${sample_prefix}.bam
 
 ##
 ## Combine per-sample results