add test reads

HCGB-IGTP · Aug 25, 2022 · 5af4a56 · 5af4a56
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diff --git a/subset2test/subset_PE/rep_1_R1.fq.gz b/subset2test/subset_PE/rep_1_R1.fq.gz
diff --git a/subset2test/subset_PE/rep_1_R2.fq.gz b/subset2test/subset_PE/rep_1_R2.fq.gz
diff --git a/subset2test/subset_PE/rep_2_R1.fq.gz b/subset2test/subset_PE/rep_2_R1.fq.gz
diff --git a/subset2test/subset_PE/rep_2_R2.fq.gz b/subset2test/subset_PE/rep_2_R2.fq.gz
diff --git a/subset2test/subset_PE/rep_3_R1.fq.gz b/subset2test/subset_PE/rep_3_R1.fq.gz
diff --git a/subset2test/subset_PE/rep_3_R2.fq.gz b/subset2test/subset_PE/rep_3_R2.fq.gz
diff --git a/subset2test/subset_PE/rep_4_R1.fq.gz b/subset2test/subset_PE/rep_4_R1.fq.gz
diff --git a/subset2test/subset_PE/rep_4_R2.fq.gz b/subset2test/subset_PE/rep_4_R2.fq.gz
diff --git a/subset2test/subset_PE/rep_5_R1.fq.gz b/subset2test/subset_PE/rep_5_R1.fq.gz
diff --git a/subset2test/subset_PE/rep_5_R2.fq.gz b/subset2test/subset_PE/rep_5_R2.fq.gz
diff --git a/subset2test/subset_SE/sample_1.fastq b/subset2test/subset_SE/sample_1.fastq
diff --git a/subset2test/subset_SE/sample_10.fastq b/subset2test/subset_SE/sample_10.fastq
diff --git a/subset2test/subset_SE/sample_2.fastq b/subset2test/subset_SE/sample_2.fastq
diff --git a/subset2test/subset_SE/sample_3.fastq b/subset2test/subset_SE/sample_3.fastq
diff --git a/subset2test/subset_SE/sample_4.fastq b/subset2test/subset_SE/sample_4.fastq
diff --git a/subset2test/subset_SE/sample_5.fastq b/subset2test/subset_SE/sample_5.fastq
diff --git a/subset2test/subset_SE/sample_6.fastq b/subset2test/subset_SE/sample_6.fastq
diff --git a/subset2test/subset_SE/sample_7.fastq b/subset2test/subset_SE/sample_7.fastq
diff --git a/subset2test/subset_SE/sample_8.fastq b/subset2test/subset_SE/sample_8.fastq
diff --git a/subset2test/subset_SE/sample_9.fastq b/subset2test/subset_SE/sample_9.fastq
diff --git a/subset2test/subset_tRNA/README b/subset2test/subset_tRNA/README
@@ -0,0 +1,18 @@
+# I used example reads provided from MintMAP v2 to create random susbets
+# https://cm.jefferson.edu/mintmap/
+# https://cm.jefferson.edu/?smd_process_download=1&download_id=8044
+
+for i in {1..5}; 
+do 
+	sample="s"$i".fastq.gz"; 
+	echo "seqtk sample -s"$i" MINTmap-v2.0-alpha/ExampleRun/exampleInput.trimmed.fastq.gz 20000 | gzip > $sample"; 
+done
+
+seqtk sample -s1 MINTmap-v2.0-alpha/ExampleRun/exampleInput.trimmed.fastq.gz 20000 | gzip > s1.fastq.gz
+seqtk sample -s2 MINTmap-v2.0-alpha/ExampleRun/exampleInput.trimmed.fastq.gz 20000 | gzip > s2.fastq.gz
+seqtk sample -s3 MINTmap-v2.0-alpha/ExampleRun/exampleInput.trimmed.fastq.gz 20000 | gzip > s3.fastq.gz
+seqtk sample -s4 MINTmap-v2.0-alpha/ExampleRun/exampleInput.trimmed.fastq.gz 20000 | gzip > s4.fastq.gz
+seqtk sample -s5 MINTmap-v2.0-alpha/ExampleRun/exampleInput.trimmed.fastq.gz 20000 | gzip > s5.fastq.gz
+
+# Use random seed each time to create different susbsets
+
diff --git a/subset2test/subset_tRNA/s1.fastq.gz b/subset2test/subset_tRNA/s1.fastq.gz
diff --git a/subset2test/subset_tRNA/s2.fastq.gz b/subset2test/subset_tRNA/s2.fastq.gz
diff --git a/subset2test/subset_tRNA/s3.fastq.gz b/subset2test/subset_tRNA/s3.fastq.gz
diff --git a/subset2test/subset_tRNA/s4.fastq.gz b/subset2test/subset_tRNA/s4.fastq.gz
diff --git a/subset2test/subset_tRNA/s5.fastq.gz b/subset2test/subset_tRNA/s5.fastq.gz
diff --git a/subset2test/test_subset.sh b/subset2test/test_subset.sh
@@ -0,0 +1,120 @@
+echo "`date` ... Starting ..."
+echo ""
+
+mkdir logs
+
+##########################################
+## test single end
+##########################################
+echo "# ------------------------------ #"
+echo "XICRA prep -i ./subset_SE/ -o XICRA_analysis --single_end"
+echo "..."
+echo ""
+XICRA prep -i ./subset_SE/ -o XICRA_analysis --single_end | tee logs/XICRA_analysis.prep.log
+echo ""
+
+echo "# ------------------------------ #"
+echo "XICRA QC -i XICRA_analysis --single_end --threads 4"
+echo "..."
+XICRA QC -i XICRA_analysis --single_end --threads 4 | tee logs/XICRA_analysis.qc.log
+echo ""
+
+echo "# ------------------------------ #"
+echo "XICRA trim -i XICRA_analysis --single_end --threads 4 --adapters_a TGGAATTCTCGGGTGCCAAGG"
+echo "..."
+XICRA trim -i XICRA_analysis --single_end --threads 4 --adapters_a TGGAATTCTCGGGTGCCAAGG | tee logs/XICRA_analysis.trim.log
+echo ""
+
+echo "# ------------------------------ #"
+echo "XICRA miRNA -i XICRA_analysis --single_end --threads 4 --software miraligner"
+echo "..."
+XICRA miRNA -i XICRA_analysis --single_end --threads 4 --software miraligner | tee logs/XICRA_analysis.miRNA.log
+echo ""
+echo "# ------------------------------ #"
+echo ""
+echo ""
+echo ""   
+echo "`date` ... Single End Test finished ..."
+echo ""
+echo ""
+echo ""
+echo ""
+##########################################
+
+##########################################
+## test paired-end
+##########################################
+
+echo "`date` ... Starting PE test..."
+
+echo "# ------------------------------ #"
+echo "XICRA prep -i ./subset_PE/ -o XICRA_analysis_PE"
+echo "..."
+XICRA prep -i ./subset_PE/ -o XICRA_analysis_PE | tee logs/XICRA_analysis_PE.prep.log
+echo ""
+
+echo "# ------------------------------ #"
+echo "XICRA QC -i XICRA_analysis_PE --threads 4"
+echo "..."
+XICRA QC -i XICRA_analysis_PE --threads 4 | tee logs/XICRA_analysis_PE.qc.log
+echo ""
+
+# ATTENTION: NO need to trim these reads as these are simulated reads
+echo "# ------------------------------ #"
+echo "XICRA join -i XICRA_analysis_PE --threads 4 --noTrim"
+echo "..."
+XICRA join -i XICRA_analysis_PE --threads 4 --noTrim | tee logs/XICRA_analysis_PE.join.log
+echo ""
+
+echo "# ------------------------------ #"
+echo "XICRA miRNA -i XICRA_analysis_PE --threads 4 --software miraligner"
+echo "..."
+XICRA miRNA -i XICRA_analysis_PE --threads 4 --software miraligner | tee logs/XICRA_analysis_PE.miRNA.log
+echo "" 
+
+echo ""   
+echo "`date` ... Paired End Test finished ..."
+echo ""   
+echo "# ------------------------------ #"
+echo ""
+echo ""
+echo ""
+echo ""
+echo ""
+echo ""
+##########################################
+
+##########################################
+## test tRNA analysis
+##########################################
+echo ""   
+echo "# ------------------------------ #"
+echo "XICRA prep -i ./subset_tRNA/ -o XICRA_analysis_tRNA --single_end"
+echo "..."
+echo ""
+XICRA prep -i ./subset_tRNA/ -o XICRA_analysis_tRNA --single_end | tee logs/XICRA_analysis_tRNA.prep.log
+echo ""
+
+echo "# ------------------------------ #"
+echo "XICRA QC -i XICRA_analysis_tRNA --single_end --threads 4"
+echo "..."
+XICRA QC -i XICRA_analysis_tRNA --single_end --threads 4 | tee logs/XICRA_analysis_tRNA.qc.log
+echo ""
+
+# ATTENTION: NO need to trim these reads as these are simulated reads
+
+echo "# ------------------------------ #"
+echo "XICRA tRNA -i XICRA_analysis_tRNA --single_end --threads 4 --software mintmap"
+echo "..."
+XICRA tRNA -i XICRA_analysis_tRNA --noTrim --single_end --threads 4 --software mintmap | tee logs/XICRA_analysis_tRNA.tRNA.log
+echo ""
+echo "# ------------------------------ #"
+echo ""
+echo ""
+echo ""   
+echo "`date` ... tRNA Single End Test finished ..."
+
+
+echo ""   
+echo "`date` ... Finished ..."
+##########################################