12_Pre-processing_expression_in_allele_specific_truncated_genes_complete ├── bin │   └── single_end_RNAseq_alignment.sh ├── input │   ├── HGAP3_Tb427v10.dict │   ├── HGAP3_Tb427v10.fasta │   ├── HGAP3_Tb427v10.fasta.fai │   ├── concatenated_HGAP3_Tb427v9.9_without_allelic_variants_core.hap │   ├── reads │   │   ├── SRR1272136.fastq.gz │   │   ├── SRR1272137.fastq.gz │   │   ├── SRR1272138.fastq.gz │   │   ├── SRR1272145.fastq.gz │   │   ├── SRR1272146.fastq.gz │   │   └── SRR1272147.fastq.gz │   └── var_corrected.untrimmed_to_HGAP3_Tb427v10_all.q20.dp10.Ns_removed.het.vcf ├── output │   ├── ASEReadCounts │   │   ├── Jensen_RNAseq_cutadapt_bwa_merged.RG_ASER_Counts.tsv │   │   └── Jensen_ribofoot_cutadapt_bwa_merged.RG_ASER_Counts.tsv │   ├── alignments │   │   ├── Jensen_RNAseq_cutadapt_bwa_merged.RG.bam │   │   ├── Jensen_RNAseq_cutadapt_bwa_merged.RG.bam.bai │   │   ├── Jensen_RNAseq_cutadapt_bwa_merged.bam │   │   ├── Jensen_ribofoot_cutadapt_bwa_merged.RG.bam │   │   ├── Jensen_ribofoot_cutadapt_bwa_merged.RG.bam.bai │   │   ├── Jensen_ribofoot_cutadapt_bwa_merged.bam │   │   ├── SRR1272136_cutadapt_to_HGAP3_Tb427v10_bwa.rmdup.metrics.txt │   │   ├── SRR1272136_cutadapt_to_HGAP3_Tb427v10_bwa.rmdup.sorted.bam │   │   ├── SRR1272136_cutadapt_to_HGAP3_Tb427v10_bwa.rmdup.sorted.bam.bai │   │   ├── SRR1272137_cutadapt_to_HGAP3_Tb427v10_bwa.rmdup.metrics.txt │   │   ├── SRR1272137_cutadapt_to_HGAP3_Tb427v10_bwa.rmdup.sorted.bam │   │   ├── SRR1272137_cutadapt_to_HGAP3_Tb427v10_bwa.rmdup.sorted.bam.bai │   │   ├── SRR1272138_cutadapt_to_HGAP3_Tb427v10_bwa.rmdup.metrics.txt │   │   ├── SRR1272138_cutadapt_to_HGAP3_Tb427v10_bwa.rmdup.sorted.bam │   │   ├── SRR1272138_cutadapt_to_HGAP3_Tb427v10_bwa.rmdup.sorted.bam.bai │   │   ├── SRR1272145_cutadapt_to_HGAP3_Tb427v10_bwa.rmdup.metrics.txt │   │   ├── SRR1272145_cutadapt_to_HGAP3_Tb427v10_bwa.rmdup.sorted.bam │   │   ├── SRR1272145_cutadapt_to_HGAP3_Tb427v10_bwa.rmdup.sorted.bam.bai │   │   ├── SRR1272146_cutadapt_to_HGAP3_Tb427v10_bwa.rmdup.metrics.txt │   │   ├── SRR1272146_cutadapt_to_HGAP3_Tb427v10_bwa.rmdup.sorted.bam │   │   ├── SRR1272146_cutadapt_to_HGAP3_Tb427v10_bwa.rmdup.sorted.bam.bai │   │   ├── SRR1272147_cutadapt_to_HGAP3_Tb427v10_bwa.rmdup.metrics.txt │   │   ├── SRR1272147_cutadapt_to_HGAP3_Tb427v10_bwa.rmdup.sorted.bam │   │   └── SRR1272147_cutadapt_to_HGAP3_Tb427v10_bwa.rmdup.sorted.bam.bai │   ├── bwa_index │   │   ├── HGAP3_Tb427v10.fasta.amb │   │   ├── HGAP3_Tb427v10.fasta.ann │   │   ├── HGAP3_Tb427v10.fasta.bwt │   │   ├── HGAP3_Tb427v10.fasta.pac │   │   └── HGAP3_Tb427v10.fasta.sa │   ├── cuadapted_reads │   │   ├── SRR1272136_cutadapt.fq.gz │   │   ├── SRR1272137_cutadapt.fq.gz │   │   ├── SRR1272138_cutadapt.fq.gz │   │   ├── SRR1272145_cutadapt.fq.gz │   │   ├── SRR1272146_cutadapt.fq.gz │   │   └── SRR1272147_cutadapt.fq.gz │   ├── filtered_HAP │   │   ├── concatenated_HGAP3_Tb427v10_core.hap │   │   └── concatenated_HGAP3_Tb427v10_core_rmBLOCK.hap │   └── filtered_VCF │   ├── var_corrected.untrimmed_to_HGAP3_Tb427v10_all.q20.dp10.Ns_removed.het.onlySNPs.vcf │   └── var_corrected.untrimmed_to_HGAP3_Tb427v10_all.q20.dp10.Ns_removed.het.onlySNPs.vcf.idx └── run.sh 10 directories, 54 files