diff bowtie_transcriptome_wrapper/bowtie_transcriptome_wrapper.py @ 8:f6ef1c85b045 draft

Uploaded

--- a/bowtie_transcriptome_wrapper/bowtie_transcriptome_wrapper.py	Fri Apr 22 11:08:21 2022 +0000
+++ b/bowtie_transcriptome_wrapper/bowtie_transcriptome_wrapper.py	Fri May 13 09:53:29 2022 +0000
@@ -412,9 +412,13 @@
         try:
             # prepare actual mapping commands
             if options.paired == 'paired':
-                cmd2 = 'bowtie %s %s -1 %s -2 %s > %s' % ( aligning_cmds, ref_file_name, options.input1, options.input2, options.output )
+                # cmd2 = 'bowtie %s %s -1 %s -2 %s > %s | samtools view -b -S > %s' % ( aligning_cmds, ref_file_name, options.input1, options.input2, options.output, options.output )
+                cmd2 = 'bowtie %s %s -1 %s -2 %s > %s ' % ( aligning_cmds, ref_file_name, options.input1, options.input2, options.output )
+
             else:
-                cmd2 = 'bowtie %s %s %s > %s' % ( aligning_cmds, ref_file_name, options.input1, options.output )
+                # cmd2 = 'bowtie %s %s %s > %s | samtools view -b -S > %s' % ( aligning_cmds, ref_file_name, options.input1, options.output, options.output )
+                cmd2 = 'bowtie %s %s %s > %s ' % ( aligning_cmds, ref_file_name, options.input1, options.output )
+
             # align
             tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name
             with open(tmp, 'w') as tmp_stderr: