Added counting postprocessing steps

README.md

@@ -136,5 +136,17 @@ Command run:
 cd /storage/schu/ProjectGroups/RNA/Data/RNASequencing/Novogene/NHHW162910/alignments/bams/bamsSortedByName
 ```
 ```bash
-featureCounts -Q 255 -T 6 -p -a /storage/scic/Data/External/Bioinformatics/Rat/Genomes/rn5_Mar2012/annotation/annRefSeq_rn5_20Apr2016.gtf -o /storage/schu/ProjectGroups/RNA/Data/RNASequencing/Novogene/NHHW162910/gene_counts/gene_counts.txt $(echo *.bam)
+featureCounts -Q 255 -T 6 -p -a /storage/scic/Data/External/Bioinformatics/Rat/Genomes/rn5_Mar2012/annotation/annRefSeq_rn5_20Apr2016.gtf -o /storage/schu/ProjectGroups/RNA/Data/RNASequencing/Novogene/NHHW162910/gene_counts/gene_counts_130117.txt $(echo *.bam)
+```
+#### Extract mapped features only
+Once the counting of the features/genes is done, we extract only those which have at least one read mapped to them:
+
+```bash
+awk -F"\t" 'OFS="\t"{if(($7+$8+$9+$10+$11+$12+$13+$14+$15+$16+$17+$18+$19+$20+$21+$22)>0){print $1,$7,$8,$9,$10,$11,$12,$13,$14,$15,$16,$17,$18,$19,$20,$21,$22}}' gene_counts_130117.txt > gene_counts_130117_only_mapped.txt
+```
+
+Then we add a header to that file with the sample names:
+
+```bash
+paste -d '\t' <(echo "gene_name") <(head -1 gene_counts_130117.txt.summary | cut -f2-) | cat - gene_counts_130117_only_mapped.txt > gene_counts_130117_only_mapped_with_header.txt
 ```