debugging smartseq in verbose mode (bdd350f7) · Commits · github_fork / Universc

launch_universc.sh

+9 −0

Original line number	Diff line number	Diff line
		@@ -3350,6 +3350,12 @@ else
		mv $crIN/parsed_R2.fastq ${convR2}
		mv $crIN/parsed_I1.fastq ${convI1}
		mv $crIN/parsed_I2.fastq ${convI2}
		if [[ $verbose ]]; then
		cp ${convR1} $crIN/parsed_R1.fastq
		cp ${convR1} $crIN/parsed_R1.fastq
		cp ${convR1} $crIN/parsed_R1.fastq
		cp ${convR1} $crIN/parsed_R1.fastq
		fi

		echo " ...concatencate barcodes to R1 from I1 and I2 index files"
		# concatenate barcocdes from dual indexes to R1 as barcode (bases 1-16)
		@@ -3357,6 +3363,9 @@ else

		#returns a combined R1 file with I1-I2-R1 concatenated (I1 and I2 are R1 barcode)
		mv $crIN/Concatenated_File.fastq ${convR1}
		if [[ $verbose ]]; then
		cp ${convR1} $crIN/Concatenated_File.fastq
		fi

		#convert TSO to expected length for 10x 5' (TSS in R1 from base 39)
		echo " handling $convFile ..."