# /projectnb/wax-es/routines/BIN/stringtie MS329_433.sorted.filtered.unspliced.bam -o MS329_433.NOREF.unspliced.gtf
# StringTie version 3.0.1
chr10	StringTie	transcript	76532263	76532979	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "5.991632"; FPKM "19952.154297"; TPM "14203.575195";
chr10	StringTie	exon	76532263	76532979	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "5.991632";
chr11	StringTie	transcript	69026141	69026379	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; cov "6.991632"; FPKM "23282.158203"; TPM "16574.144531";
chr11	StringTie	exon	69026141	69026379	1000	+	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "1"; cov "6.991632";
chr11	StringTie	transcript	109256573	109256933	1000	+	.	gene_id "STRG.3"; transcript_id "STRG.3.1"; cov "5.814404"; FPKM "19361.984375"; TPM "13783.444336";
chr11	StringTie	exon	109256573	109256933	1000	+	.	gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "1"; cov "5.814404";
chr14	StringTie	transcript	33953463	33953808	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.1"; cov "10.040462"; FPKM "33434.769531"; TPM "23801.605469";
chr14	StringTie	exon	33953463	33953808	1000	-	.	gene_id "STRG.4"; transcript_id "STRG.4.1"; exon_number "1"; cov "10.040462";
chr14	StringTie	transcript	103242671	103242896	1000	+	.	gene_id "STRG.5"; transcript_id "STRG.5.1"; cov "6.778761"; FPKM "22573.294922"; TPM "16069.519531";
chr14	StringTie	exon	103242671	103242896	1000	+	.	gene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "1"; cov "6.778761";
chr15	StringTie	transcript	55252038	55252609	1000	+	.	gene_id "STRG.6"; transcript_id "STRG.6.1"; cov "4.942307"; FPKM "16457.898438"; TPM "11716.078125";
chr15	StringTie	exon	55252038	55252609	1000	+	.	gene_id "STRG.6"; transcript_id "STRG.6.1"; exon_number "1"; cov "4.942307";
chr15	StringTie	transcript	88292385	88292628	1000	+	.	gene_id "STRG.7"; transcript_id "STRG.7.1"; cov "8.967213"; FPKM "29860.849609"; TPM "21257.394531";
chr15	StringTie	exon	88292385	88292628	1000	+	.	gene_id "STRG.7"; transcript_id "STRG.7.1"; exon_number "1"; cov "8.967213";
chr18	StringTie	transcript	35176429	35176987	1000	+	.	gene_id "STRG.8"; transcript_id "STRG.8.1"; cov "11.797853"; FPKM "39286.890625"; TPM "27967.621094";
chr18	StringTie	exon	35176429	35176987	1000	+	.	gene_id "STRG.8"; transcript_id "STRG.8.1"; exon_number "1"; cov "11.797853";
chr19	StringTie	transcript	23139305	23141545	1000	-	.	gene_id "STRG.9"; transcript_id "STRG.9.1"; cov "26.234270"; FPKM "87360.203125"; TPM "62190.140625";
chr19	StringTie	exon	23139305	23141545	1000	-	.	gene_id "STRG.9"; transcript_id "STRG.9.1"; exon_number "1"; cov "26.234270";
chr19	StringTie	transcript	45661886	45662227	1000	-	.	gene_id "STRG.10"; transcript_id "STRG.10.1"; cov "29.827486"; FPKM "99325.625000"; TPM "70708.109375";
chr19	StringTie	exon	45661886	45662227	1000	-	.	gene_id "STRG.10"; transcript_id "STRG.10.1"; exon_number "1"; cov "29.827486";
chr19	StringTie	transcript	46077341	46077616	1000	-	.	gene_id "STRG.11"; transcript_id "STRG.11.1"; cov "4.793478"; FPKM "15962.297852"; TPM "11363.269531";
chr19	StringTie	exon	46077341	46077616	1000	-	.	gene_id "STRG.11"; transcript_id "STRG.11.1"; exon_number "1"; cov "4.793478";
chr1	StringTie	transcript	154441733	154442345	1000	-	.	gene_id "STRG.12"; transcript_id "STRG.12.1"; cov "5.000000"; FPKM "16650.017578"; TPM "11852.843750";
chr1	StringTie	exon	154441733	154442345	1000	-	.	gene_id "STRG.12"; transcript_id "STRG.12.1"; exon_number "1"; cov "5.000000";
chr1	StringTie	transcript	186434605	186434857	1000	-	.	gene_id "STRG.13"; transcript_id "STRG.13.1"; cov "20.794466"; FPKM "69245.640625"; TPM "49294.710938";
chr1	StringTie	exon	186434605	186434857	1000	-	.	gene_id "STRG.13"; transcript_id "STRG.13.1"; exon_number "1"; cov "20.794466";
chr3	StringTie	transcript	42888041	42888683	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.1"; cov "13.000000"; FPKM "43290.042969"; TPM "30817.394531";
chr3	StringTie	exon	42888041	42888683	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.1"; exon_number "1"; cov "13.000000";
chr3	StringTie	transcript	98636476	98636863	1000	-	.	gene_id "STRG.15"; transcript_id "STRG.15.1"; cov "9.216495"; FPKM "30690.957031"; TPM "21848.335938";
chr3	StringTie	exon	98636476	98636863	1000	-	.	gene_id "STRG.15"; transcript_id "STRG.15.1"; exon_number "1"; cov "9.216495";
chr4	StringTie	transcript	115721956	115722451	1000	-	.	gene_id "STRG.16"; transcript_id "STRG.16.1"; cov "10.983871"; FPKM "36576.328125"; TPM "26038.021484";
chr4	StringTie	exon	115721956	115722451	1000	-	.	gene_id "STRG.16"; transcript_id "STRG.16.1"; exon_number "1"; cov "10.983871";
chr5	StringTie	transcript	123425883	123426304	1000	-	.	gene_id "STRG.17"; transcript_id "STRG.17.1"; cov "6.601896"; FPKM "21984.335938"; TPM "15650.248047";
chr5	StringTie	exon	123425883	123426304	1000	-	.	gene_id "STRG.17"; transcript_id "STRG.17.1"; exon_number "1"; cov "6.601896";
chr6	StringTie	transcript	71814085	71814518	1000	+	.	gene_id "STRG.18"; transcript_id "STRG.18.1"; cov "10.546082"; FPKM "35118.488281"; TPM "25000.212891";
chr6	StringTie	exon	71814085	71814518	1000	+	.	gene_id "STRG.18"; transcript_id "STRG.18.1"; exon_number "1"; cov "10.546082";
chr6	StringTie	transcript	100090463	100090675	1000	-	.	gene_id "STRG.19"; transcript_id "STRG.19.1"; cov "18.000000"; FPKM "59940.054688"; TPM "42670.238281";
chr6	StringTie	exon	100090463	100090675	1000	-	.	gene_id "STRG.19"; transcript_id "STRG.19.1"; exon_number "1"; cov "18.000000";
chr7	StringTie	transcript	19880240	19880551	1000	-	.	gene_id "STRG.20"; transcript_id "STRG.20.1"; cov "5.967949"; FPKM "19873.289062"; TPM "14147.433594";
chr7	StringTie	exon	19880240	19880551	1000	-	.	gene_id "STRG.20"; transcript_id "STRG.20.1"; exon_number "1"; cov "5.967949";
chr7	StringTie	transcript	30092012	30092292	1000	+	.	gene_id "STRG.21"; transcript_id "STRG.21.1"; cov "41.935944"; FPKM "139646.828125"; TPM "99412.039062";
chr7	StringTie	exon	30092012	30092292	1000	+	.	gene_id "STRG.21"; transcript_id "STRG.21.1"; exon_number "1"; cov "41.935944";
chr7	StringTie	transcript	106187441	106187845	1000	-	.	gene_id "STRG.22"; transcript_id "STRG.22.1"; cov "6.234568"; FPKM "20761.132812"; TPM "14779.471680";
chr7	StringTie	exon	106187441	106187845	1000	-	.	gene_id "STRG.22"; transcript_id "STRG.22.1"; exon_number "1"; cov "6.234568";
chr7	StringTie	transcript	119182714	119182981	1000	+	.	gene_id "STRG.23"; transcript_id "STRG.23.1"; cov "57.477612"; FPKM "191400.640625"; TPM "136254.625000";
chr7	StringTie	exon	119182714	119182981	1000	+	.	gene_id "STRG.23"; transcript_id "STRG.23.1"; exon_number "1"; cov "57.477612";
chr7	StringTie	transcript	142164339	142164629	1000	+	.	gene_id "STRG.24"; transcript_id "STRG.24.1"; cov "37.945019"; FPKM "126357.046875"; TPM "89951.281250";
chr7	StringTie	exon	142164339	142164629	1000	+	.	gene_id "STRG.24"; transcript_id "STRG.24.1"; exon_number "1"; cov "37.945019";
chr7	StringTie	transcript	152404674	152404940	1000	+	.	gene_id "STRG.25"; transcript_id "STRG.25.1"; cov "4.970037"; FPKM "16550.238281"; TPM "11781.814453";
chr7	StringTie	exon	152404674	152404940	1000	+	.	gene_id "STRG.25"; transcript_id "STRG.25.1"; exon_number "1"; cov "4.970037";
chr8	StringTie	transcript	3466130	3466519	1000	-	.	gene_id "STRG.26"; transcript_id "STRG.26.1"; cov "8.617949"; FPKM "28697.796875"; TPM "20429.441406";
chr8	StringTie	exon	3466130	3466519	1000	-	.	gene_id "STRG.26"; transcript_id "STRG.26.1"; exon_number "1"; cov "8.617949";
chr8	StringTie	transcript	50802818	50803034	1000	+	.	gene_id "STRG.27"; transcript_id "STRG.27.1"; cov "7.926267"; FPKM "26394.496094"; TPM "18789.761719";
chr8	StringTie	exon	50802818	50803034	1000	+	.	gene_id "STRG.27"; transcript_id "STRG.27.1"; exon_number "1"; cov "7.926267";
chr8	StringTie	transcript	102832139	102832367	1000	+	.	gene_id "STRG.28"; transcript_id "STRG.28.1"; cov "4.978166"; FPKM "16577.310547"; TPM "11801.084961";
chr8	StringTie	exon	102832139	102832367	1000	+	.	gene_id "STRG.28"; transcript_id "STRG.28.1"; exon_number "1"; cov "4.978166";
chr9	StringTie	transcript	19820623	19820903	1000	-	.	gene_id "STRG.29"; transcript_id "STRG.29.1"; cov "12.000000"; FPKM "39960.039062"; TPM "28446.824219";
chr9	StringTie	exon	19820623	19820903	1000	-	.	gene_id "STRG.29"; transcript_id "STRG.29.1"; exon_number "1"; cov "12.000000";
chr9	StringTie	transcript	106672763	106673714	1000	-	.	gene_id "STRG.30"; transcript_id "STRG.30.1"; cov "12.559874"; FPKM "41824.421875"; TPM "29774.044922";
chr9	StringTie	exon	106672763	106673714	1000	-	.	gene_id "STRG.30"; transcript_id "STRG.30.1"; exon_number "1"; cov "12.559874";
chrX	StringTie	transcript	136845057	136845681	1000	+	.	gene_id "STRG.31"; transcript_id "STRG.31.1"; cov "4.904000"; FPKM "16330.335938"; TPM "11625.269531";
chrX	StringTie	exon	136845057	136845681	1000	+	.	gene_id "STRG.31"; transcript_id "STRG.31.1"; exon_number "1"; cov "4.904000";