diff --git a/assets/multiqc_config.yaml b/assets/multiqc_config.yaml
index c83e60d5ead2f356c11ab8ca3964173926ce4331..881762c76d52fc1a873314941f6d04afa91cbd92 100644
--- a/assets/multiqc_config.yaml
+++ b/assets/multiqc_config.yaml
@@ -4,6 +4,9 @@ title: "My Title"
 #subtitle: "A subtitle to go underneath in grey"
 intro_text: "This MultiQC report summarise Quality Control analysis results."
 
+report_comment: >
+  You can find detailed guidance on how to interpret the following graphs in the <a href="https://bios4biol.pages.mia.inra.fr/Help4MultiQC/" target="_blank"><strong>Help4MultiQC GitBook</strong></a>.  
+  Developed by some members of the CATI Bios4Biol team at INRAE, this resource provides valuable insights into data interpretation. While it was not specifically created for this report, it offers complementary information that may help deepen your understanding of the presented data.
 
 show_analysis_paths: False
 show_analysis_time: False
@@ -33,7 +36,7 @@ table_columns_visible:
 extra_fn_clean_exts:
   - "_qualimap_results"
   - "_filtered"
-  - "_unmerged"
+  - "_sorted"
   - "_flagstat"
   - "_subset"
   - "_screen"
diff --git a/conf/base.config b/conf/base.config
index 0be9913b3373459a9a96d6bec470e25f99a5abe1..6f435ae248775f746302bef4b4e8c1be608d7a3c 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -133,7 +133,8 @@ process {
 
 		publishDir = [
 			path: "${params.outdir}/alignment/bwa",
-			mode: 'copy'
+			mode: 'copy',
+			pattern: '*.log',
 		]
 	}
 
@@ -223,6 +224,14 @@ process {
 		].join(' ')
 	}
 
+	withName: 'GET_UNMAPPED|GET_UNMAPPED_SALMON' {
+		publishDir = [
+			path: "${params.outdir}/alignment/unmapped",
+			mode: 'copy',
+			pattern: "*.fastq.gz"
+		]
+	}
+
 	// ----- WithLabel
 	withLabel: littleJob {
 		executor = 'local'
@@ -235,17 +244,15 @@ process {
 	    time = { checkMax( 24.h * task.attempt, 'time' ) }
 	}
 
-	withLabel: alignment {
-		publishDir = [
-			path: "${params.outdir}/alignment/samtools",
-			mode: 'copy'
-		]
+	withLabel: seqkit {
+		module = toolsModuleHash['SEQKIT']
 	}
 
 	withLabel: alignmentStats {
 		publishDir = [
 			path: "${params.outdir}/alignmentStats/samtools",
-			mode: 'copy'
+			mode: 'copy',
+			pattern: "*.txt"
 		]
 	}
 
@@ -382,15 +389,6 @@ process {
 	    ]
     }
 
-	withName: 'MD5SUM_FASTQ|MD5SUM_INDEX' {
-		time = { checkMax( 3.h * task.attempt * params.resource_factor, 'time' ) }
-		publishDir = [
-            path: "${params.outdir}/fastq",
-            mode: 'copy',
-            pattern: "*.md5sum"
-        ]
-	}
-
 	withName: QUALIMAP {
 		module = toolsModuleHash['QUALIMAP']
 		cpus = { checkMax( 8 * task.attempt, 'cpus' ) }
diff --git a/conf/dependencies_genobioinfo.config b/conf/dependencies_genobioinfo.config
index 6719d125df26fb45a759676be8da66ee4e1e633b..8ad013ca7cfaea64b738ca1809c79f7da887e6e9 100644
--- a/conf/dependencies_genobioinfo.config
+++ b/conf/dependencies_genobioinfo.config
@@ -12,6 +12,7 @@ toolsModuleHash['PICARD'] = ['statistics/R/4.3.0', 'devel/java/17.0.6', 'bioinfo
 // ----- RNA ----- //
 toolsModuleHash['SALMON'] = ['bioinfo/Salmon/1.10.0']  // version upgraded face to genologin
 toolsModuleHash['STAR'] = ['bioinfo/STAR/2.7.5a']    // version upgraded face to genologin
+toolsModuleHash['SEQKIT'] = ['bioinfo/SeqKit/2.9.0']
 
 // ----- DNA ----- //
 toolsModuleHash['BWA'] = ['bioinfo/bwa/0.7.17']
diff --git a/modules/local/module_core.nf b/modules/local/module_core.nf
index be422b7272cc4b22fc6dea606a59338878b4e0f6..fba9ca106c8d56593f34aacdc63c1322d9bd3ea6 100644
--- a/modules/local/module_core.nf
+++ b/modules/local/module_core.nf
@@ -147,6 +147,30 @@ process DUPLICATED_READS {
 	'''
 }
 
+process GET_UNMAPPED {
+	tag "$sample"
+	
+	label 'samtools'
+
+	input:
+		tuple val(sample), path(sorted_bam)	// [[id], [files, ...]]
+
+	output:
+		tuple val(sample), path("*.log"), emit: log
+		tuple val(sample), path("*.fastq.gz"), emit: fastq_gz
+		path("versions.yml"), emit: versions
+
+	script:
+	def analyse_type = task.ext.analyse_type ?: params.default_label
+	"""
+		samtools fastq -f 4 ${sorted_bam} 2>> ${sample}_unmapped.log | gzip -c > ${sample}_unmapped.fastq.gz
+	
+	cat <<-END_VERSIONS > versions.yml
+	${analyse_type} - samtools: \$(samtools --version 2>&1 | sed '/^.*samtools/!d; s/.* //')
+	END_VERSIONS
+	"""
+}
+
 process MERGE_LANES {	
 	tag "$sample"
 	
diff --git a/modules/local/module_dna.nf b/modules/local/module_dna.nf
index 7355e77408d5afec5fcf5c9766cf7cb4d600422c..6dc45428e37bba961f22546c77b9e3e005c3d2bd 100644
--- a/modules/local/module_dna.nf
+++ b/modules/local/module_dna.nf
@@ -55,7 +55,6 @@ process SAMTOOLS_SORT {
 	tag "$sample"
 	
 	label 'samtools'
-	label 'alignment'
 
 	input:
 		tuple val(sample), path(bam)
@@ -64,12 +63,11 @@ process SAMTOOLS_SORT {
 		tuple val(sample), path("*.log"), emit: log
 		tuple val(sample), path("*.bam"), emit: bam
 		path("versions.yml"), emit: versions
-		//path("*.bam"), emit: bam
 
-	script:	// Pourquoi unmerged ??? https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/blob/master/workflows/components/bwa.py#L97
+	script:	
 	def analyse_type = task.ext.analyse_type ?: params.default_label
 	"""	
-		samtools sort ${bam} -o ${sample}_unmerged.bam 2>> ${sample}.log
+		samtools sort ${bam} -o ${sample}_sorted.bam 2>> ${sample}.log
 	
 	cat <<-END_VERSIONS > versions.yml
 	${analyse_type} - samtools: \$(samtools --version 2>&1 | sed '/^.*samtools/!d; s/.* //')
diff --git a/modules/local/module_rna.nf b/modules/local/module_rna.nf
index 5201617b37b9cf2574f79ce8b66c1a553ca1f613..dd38c703d3b76503b5e4eaa772af16edd07d19b6 100644
--- a/modules/local/module_rna.nf
+++ b/modules/local/module_rna.nf
@@ -58,6 +58,38 @@ process SALMON_QUANT {
     """
 }
 
+process GET_UNMAPPED_SALMON {
+	tag "$sample"
+	
+	label 'seqkit'
+
+	input:
+		tuple val(sample), path(reads)	// [[id], [R1, R2]]
+        tuple val(sample), path(salmon_results)
+
+	output:
+		tuple val(sample), path("*.fastq.gz"), emit: fastq_gz, optional: true
+		path("versions.yml"), emit: versions
+
+	script:
+    def R1 = reads.find { it =~ /.*_R1_.*/}
+    def R2 = reads.find { it =~ /.*_R2_.*/}
+    def analyse_type = task.ext.analyse_type ?: params.default_label
+	"""
+		grep 'u\$' ${salmon_results}/aux_info/unmapped_names.txt | cut -d' ' -f1 > unmapped_id
+
+        seqkit grep -f unmapped_id ${R1} -o unmapped_R1.fastq
+        seqkit grep -f unmapped_id ${R2} -o unmapped_R2.fastq
+
+        cat unmapped_R1.fastq unmapped_R2.fastq | gzip -c > ${sample}_unmapped.fastq.gz
+        
+	cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+    ${analyse_type} - seqkit: \$( seqkit version | sed 's/seqkit v//' )
+    END_VERSIONS
+	"""
+}
+
 process STAR_INDEX {
     tag "$params.project"
     label "star"
diff --git a/sub-workflows/local/dna_qc.nf b/sub-workflows/local/dna_qc.nf
index b7d5e6a871b500f66bcd30625ca6272bd7f2f1a4..23892c227786a4ad11c936d855e5252924a4c15f 100644
--- a/sub-workflows/local/dna_qc.nf
+++ b/sub-workflows/local/dna_qc.nf
@@ -10,12 +10,12 @@
 // -------------------------------------------------
 // 					MODULES
 // -------------------------------------------------
-include { 	BWA_ALIGNMENT;
-			SAMTOOLS_VIEW;
-			SAMTOOLS_SORT;
-			SAMTOOLS_FLAGSTATS;
-} from "$baseDir/modules/local/module_dna.nf"
-include { 	QUALIMAP } from "${params.shared_modules}/qualimap.nf"
+include { 	BWA_ALIGNMENT 		} from "$baseDir/modules/local/module_dna.nf"
+include {	SAMTOOLS_VIEW 		} from "$baseDir/modules/local/module_dna.nf"
+include {	SAMTOOLS_SORT 		} from "$baseDir/modules/local/module_dna.nf"
+include {	SAMTOOLS_FLAGSTATS	} from "$baseDir/modules/local/module_dna.nf"
+include { 	GET_UNMAPPED		} from "$baseDir/modules/local/module_core.nf"
+include { 	QUALIMAP 			} from "${params.shared_modules}/qualimap.nf"
 
 // -------------------------------------------------
 // 					WORKFLOW
@@ -33,6 +33,7 @@ workflow DNA_QC {
 			SAMTOOLS_SORT(SAMTOOLS_VIEW.out.bam)
 			SAMTOOLS_FLAGSTATS(SAMTOOLS_VIEW.out.bam)
 			QUALIMAP(SAMTOOLS_SORT.out.bam)
+			GET_UNMAPPED(SAMTOOLS_SORT.out.bam)
 
 			qualimap_report_emitted =  QUALIMAP.out.report
 			flagstats_output_emitted = SAMTOOLS_FLAGSTATS.out.txt
diff --git a/sub-workflows/local/rna_qc.nf b/sub-workflows/local/rna_qc.nf
index bfac0d84b663ecaccc7745fba210e6c3c501b79c..43ed440859f22177c2f355e834d6503e0bb34fdb 100644
--- a/sub-workflows/local/rna_qc.nf
+++ b/sub-workflows/local/rna_qc.nf
@@ -22,10 +22,12 @@ include { 	STAR_INDEX;
 			SALMON_INDEX;
 			SALMON_QUANT;
 } from "$baseDir/modules/local/module_rna.nf"
+include { GET_UNMAPPED_SALMON } from "$baseDir/modules/local/module_rna.nf"
 include { 	SAMTOOLS_VIEW;
 			SAMTOOLS_SORT;
 			SAMTOOLS_FLAGSTATS;
 } from "$baseDir/modules/local/module_dna.nf"
+include { GET_UNMAPPED		} from "$baseDir/modules/local/module_core.nf"
 include { DNA_QC as BWA		} from "$baseDir/sub-workflows/local/dna_qc.nf"
 include { QUALIMAP 			} from "${params.shared_modules}/qualimap.nf"
 include { SAMTOOLS_FAIDX	} from "${params.shared_modules}/samtools.nf"
@@ -60,6 +62,7 @@ workflow RNA_QC {
 			SAMTOOLS_VIEW(STAR_ALIGN.out.sam)
 			SAMTOOLS_SORT(SAMTOOLS_VIEW.out.bam)
 			SAMTOOLS_FLAGSTATS(SAMTOOLS_VIEW.out.bam)
+			GET_UNMAPPED(SAMTOOLS_SORT.out.bam)
 			qualimap_report_emitted = QUALIMAP(SAMTOOLS_SORT.out.bam).report
 			ch_versions = ch_versions.mix(
 				STAR_ALIGN.out.versions,
@@ -108,6 +111,7 @@ workflow RNA_QC {
 					salmon_index, 
 					ch_lib_type
 				).results
+				GET_UNMAPPED_SALMON(fastq, align_results)
 				qualimap_report_emitted= Channel.empty()
 				ch_versions = ch_versions.mix(SALMON_QUANT.out.versions)
 			}
diff --git a/workflow/short_reads_qc.nf b/workflow/short_reads_qc.nf
index f02ca31d76944ecd5ce0feef4f4fba69badeb906..dee4354501f384d9b1d1c603c243fc7d8dc6064e 100644
--- a/workflow/short_reads_qc.nf
+++ b/workflow/short_reads_qc.nf
@@ -154,7 +154,7 @@ workflow SHORT_READS_QC {
 			PARSE_REPORTS(CORE.out.fastp_report, DNA_QC.out.qualimap_report, GC_BIAS.out.summary)
 		}
 
-	} else if (params.data_nature =~ 'RNA-*|TRANSCRIPTOMIC') {
+	} else if (params.data_nature =~ 'RNA*|TRANSCRIPTOMIC') {
 		RNA_QC(CORE.out.subset_fastq, ch_sortmerna_db)
 		ch_mqc = ch_mqc.mix(
 			RNA_QC.out.align_results.collect{it[1]}.ifEmpty([]),