@HD	VN:1.5	SO:coordinate
@SQ	SN:8	LN:145138636	M5:c67955b5f7815a9a1edfaa15893d3616	UR:file:/home/keita/2021_001_Taavitsainen_NatCommun/lncap_dropseq/001_data/001_reference/Homo_sapiens.GRCh38.dna.primary_assembly.fa
@RG	ID:A	SM:tiny1
@PG	ID:STAR	PN:STAR	VN:2.7.11b	CL:/home/keita/miniconda3/bin/STAR-avx2   --runThreadN 1   --genomeDir 001_data/001_reference/STAR_index_chr8_MYC_masked   --readFilesIn 006_fastq/pg_005_07_tiny1.cb.umi.qc.woAdapter.trimPolyA.fastq      --outFileNamePrefix 006_fastq/pg_006_01_tiny1.star_
@PG	ID:0	PN:TagReadWithGeneFunction	CL:TagReadWithGeneFunction INPUT=007_bam/pg_007_02_tiny1.merged.bam OUTPUT=007_bam/pg_007_03_tiny1.star_gene_exon_tagged.bam ANNOTATIONS_FILE=001_data/001_reference/genes.refFlat    GENE_NAME_TAG=gn GENE_STRAND_TAG=gs GENE_FUNCTION_TAG=gf READ_FUNCTION_TAG=XF USE_STRAND_INFO=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false	VN:2.3.0(34e6572_1555443285)
@PG	ID:1	PN:DetectBeadSubstitutionErrors	CL:DetectBeadSubstitutionErrors INPUT=[007_bam/pg_007_03_tiny1.star_gene_exon_tagged.bam] OUTPUT=007_bam/pg_007_04_tiny1.clean_substitution.bam OUTPUT_REPORT=007_bam/pg_007_04_tiny1.clean_substitution.bam.report.txt MIN_UMIS_PER_CELL=1 TMP_DIR=[007_bam/tmp]    FILTER_AMBIGUOUS=true FREQ_COMMON_SUBSTITUTION=0.8 CELL_BARCODE_TAG=XC MOLECULAR_BARCODE_TAG=XM UMI_BIAS_THRESHOLD=0.8 EDIT_DISTANCE=1 READ_MQ=10 NUM_THREADS=1 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false	VN:2.3.0(34e6572_1555443285)
@CO	Bottom-up edit distance collapse tag XC with edit distance 1 filtering ambiguous neighbors=true
TEST.2	0	8	127740348	255	44M	*	0	0	TTTAATGTAACCTTGCTAAAGGAGTGATTTCTATTTCCTTTCTT	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	XC:Z:AATACAACGGTA	MD:Z:44	XF:Z:INTRONIC	PG:Z:STAR	RG:Z:A	NH:i:1	NM:i:0	XM:Z:CCACCAAA	ZP:i:45	UQ:i:0	AS:i:43	gf:Z:INTRONIC	gn:Z:ENSG00000136997	gs:Z:+
TEST.1	0	8	127740694	255	51M	*	0	0	GAATGTCAAGAGGCGAACACACAACGTCTTGGAGCGCCAGAGGAGGAACGA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	XC:Z:AATACAACGGTA	MD:Z:51	XF:Z:CODING	PG:Z:STAR	RG:Z:A	NH:i:1	NM:i:0	XM:Z:GGAGCAAA	UQ:i:0	AS:i:50	gf:Z:CODING	gn:Z:ENSG00000136997	gs:Z:+
TEST.3	4	*	0	0	*	*	0	0	TTTTTCCCCCAAAAAATTTTT	IIIIIIIIIIIIIIIIIIIII	XC:Z:AATACAACGGTA	PG:Z:STAR	RG:Z:A	XM:Z:AAAAAAAA	ZS:i:30