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kenminsoo · Jul 28, 2023 · 8914aa6 · 8914aa6
1 parent 581433c
commit 8914aa6
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Showing 3 changed files with 3 additions and 6 deletions.
diff --git a/install/export_r_packages.sh b/install/export_r_packages.sh
diff --git a/sRNA_fragment_P1.py b/sRNA_fragment_P1.py
@@ -257,7 +257,7 @@
 ## Deduplication BAM files ##
 if remove_umis_bool == True:
     os.system('cd ' + working_dir + '; \
-              cat samples_adapters.txt | parallel --memsuspend ' + str(mem_free) + 'G -j ' + str(max_cores) + ' --progress "samtools sort --write-index -b -o sorted_{}.bam {}.bam";\
+              cat samples_adapters.txt | parallel --memsuspend ' + str(mem_free) + 'G -j ' + str(max_cores) + ' --progress "samtools sort --write-index -o sorted_{}.bam {}.bam";\
               cat samples_adapters.txt | parallel --memsuspend ' + str(mem_free) + 'G -j ' + str(max_cores) + ' --progress "mv sorted_{}.bam {}.bam";\
               cat samples_adapters.txt | parallel --memsuspend ' + str(mem_free) + 'G -j ' + str(max_cores) + ' --progress "mv sorted_{}.bam.csi {}.bam.csi";\
               cat samples_adapters.txt | parallel --memsuspend ' + str(mem_free)  + 'G --memfree ' + str(mem_free) + 'G -j ' + str(max_cores) + ' --progress "umi_tools dedup --method=unique --stdin={}.bam --log={}.logfile > dedup_{}.bam";\

diff --git a/scripts/analyze_srnafrag.py b/scripts/analyze_srnafrag.py
@@ -573,6 +573,8 @@ def decode_sequence(plate):
 
     return final_result
 
+# Normalize with RPKM
+
 # Obtain RNA-fold plots of all potential sources
 # Given the original gtf file, merged_counts, and merged id. 
 def rna_fold(merged_id, gtf, ref, filtered, cluster_tab, out_dir):