# StringTie version 2\.2\.1
# stringtie --merge -p [0-9]+ -G /[-_/a-zA-Z0-9]+\.dat -m 50 -c 0 -F 1\.0 -T 1\.0 -f 0\.01 -g 250 -o /[-_/a-zA-Z0-9]+\.dat /[-_/a-zA-Z0-9]+\.dat /[-_/a-zA-Z0-9]+\.dat
chr1\tStringTie\texon\t3189811\t3193042\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
chr1\tStringTie\texon\t3200023\t3200191\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
chr1\tStringTie\texon\t3201078\t3201809\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
chr1\tStringTie\texon\t3204563\t3207049\t1000\t-\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "Xkr4"; exon_number "[0-9]+"; ref_gene_id "Xkr4"; 
chr1\tStringTie\texon\t3212214\t3212439\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
chr1\tStringTie\texon\t3212718\t3212801\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
chr1\tStringTie\texon\t3213096\t3213242\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
chr1\tStringTie\texon\t3242634\t3243079\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
chr1\tStringTie\texon\t3243348\t3243401\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
chr1\tStringTie\texon\t3277914\t3278390\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
chr1\tStringTie\texon\t3280687\t3280741\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
chr1\tStringTie\texon\t3282761\t3282832\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
chr1\tStringTie\texon\t3290489\t3291273\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
chr1\tStringTie\texon\t3299444\t3299664\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
chr1\tStringTie\texon\t3319000\t3319051\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
chr1\tStringTie\texon\t3351241\t3351311\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
chr1\tStringTie\texon\t3355908\t3356119\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
chr1\tStringTie\texon\t3363077\t3363446\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
chr1\tStringTie\texon\t3363754\t3363849\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
chr1\tStringTie\texon\t3377212\t3377262\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
chr1\tStringTie\texon\t3386740\t3386836\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
chr1\tStringTie\texon\t3411783\t3411982\t1000\t-\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "Xkr4"; exon_number "[0-9]+"; ref_gene_id "Xkr4"; 
chr1\tStringTie\texon\t3450907\t3451109\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; 
chr1\tStringTie\texon\t3660633\t3661579\t1000\t-\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "Xkr4"; exon_number "[0-9]+"; ref_gene_id "Xkr4"; 
chr1\tStringTie\ttranscript\t3189811\t3193042\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
chr1\tStringTie\ttranscript\t3200023\t3200191\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
chr1\tStringTie\ttranscript\t3201078\t3201809\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
chr1\tStringTie\ttranscript\t3204563\t3661579\t1000\t-\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "Xkr4"; ref_gene_id "Xkr4"; 
chr1\tStringTie\ttranscript\t3212214\t3212439\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
chr1\tStringTie\ttranscript\t3212718\t3212801\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
chr1\tStringTie\ttranscript\t3213096\t3213242\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
chr1\tStringTie\ttranscript\t3242634\t3243079\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
chr1\tStringTie\ttranscript\t3243348\t3243401\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
chr1\tStringTie\ttranscript\t3277914\t3278390\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
chr1\tStringTie\ttranscript\t3280687\t3280741\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
chr1\tStringTie\ttranscript\t3282761\t3282832\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
chr1\tStringTie\ttranscript\t3290489\t3291273\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
chr1\tStringTie\ttranscript\t3299444\t3299664\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
chr1\tStringTie\ttranscript\t3319000\t3319051\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
chr1\tStringTie\ttranscript\t3351241\t3351311\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
chr1\tStringTie\ttranscript\t3355908\t3356119\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
chr1\tStringTie\ttranscript\t3363077\t3363446\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
chr1\tStringTie\ttranscript\t3363754\t3363849\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
chr1\tStringTie\ttranscript\t3377212\t3377262\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
chr1\tStringTie\ttranscript\t3386740\t3386836\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
chr1\tStringTie\ttranscript\t3450907\t3451109\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; 
chr1\tmm9_refFlat\texon\t4334224\t4340172\t\.\t-\t\.\tgene_id "Rp1"; transcript_id "Rp1"; exon_number "[0-9]+";
chr1\tmm9_refFlat\texon\t4341991\t4342162\t\.\t-\t\.\tgene_id "Rp1"; transcript_id "Rp1"; exon_number "[0-9]+";
chr1\tmm9_refFlat\texon\t4342283\t4342918\t\.\t-\t\.\tgene_id "Rp1"; transcript_id "Rp1"; exon_number "[0-9]+";
chr1\tmm9_refFlat\texon\t4350281\t4350473\t\.\t-\t\.\tgene_id "Rp1"; transcript_id "Rp1"; exon_number "[0-9]+";
chr1\tmm9_refFlat\texon\t4481009\t4482749\t\.\t-\t\.\tgene_id "Sox17"; transcript_id "Sox17"; exon_number "[0-9]+";
chr1\tmm9_refFlat\texon\t4483181\t4483547\t\.\t-\t\.\tgene_id "Sox17"; transcript_id "Sox17"; exon_number "[0-9]+";
chr1\tmm9_refFlat\texon\t4483853\t4483944\t\.\t-\t\.\tgene_id "Sox17"; transcript_id "Sox17"; exon_number "[0-9]+";
chr1\tmm9_refFlat\texon\t4485217\t4486023\t\.\t-\t\.\tgene_id "Sox17"; transcript_id "Sox17"; exon_number "[0-9]+";
chr1\tmm9_refFlat\texon\t4486372\t4486494\t\.\t-\t\.\tgene_id "Sox17"; transcript_id "Sox17"; exon_number "[0-9]+";
chr1\tmm9_refFlat\texon\t4763279\t4764597\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "[0-9]+";
chr1\tmm9_refFlat\texon\t4763279\t4764597\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "[0-9]+";
chr1\tmm9_refFlat\texon\t4763279\t4766882\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "[0-9]+";
chr1\tmm9_refFlat\texon\t4767606\t4767729\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "[0-9]+";
chr1\tmm9_refFlat\texon\t4767606\t4767729\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "[0-9]+";
chr1\tmm9_refFlat\texon\t4767606\t4767729\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "[0-9]+";
chr1\tmm9_refFlat\texon\t4772649\t4772814\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "[0-9]+";
chr1\tmm9_refFlat\texon\t4772649\t4772814\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "[0-9]+";
chr1\tmm9_refFlat\texon\t4772649\t4772814\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "[0-9]+";
chr1\tmm9_refFlat\texon\t4774032\t4774186\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "[0-9]+";
chr1\tmm9_refFlat\texon\t4774032\t4774186\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "[0-9]+";
chr1\tmm9_refFlat\texon\t4775654\t4775807\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "[0-9]+";
chr1\tmm9_refFlat\texon\t4775654\t4775807\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "[0-9]+";
chr1\tmm9_refFlat\texon\t4775654\t4775807\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "[0-9]+";
chr1\tmm9_refFlat\texon\t4797974\t4798063\t\.\t\+\t\.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "[0-9]+";
chr1\tmm9_refFlat\texon\t4798536\t4798567\t\.\t\+\t\.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "[0-9]+";
chr1\tmm9_refFlat\texon\t4818665\t4818730\t\.\t\+\t\.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "[0-9]+";
chr1\tmm9_refFlat\texon\t4820349\t4820396\t\.\t\+\t\.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "[0-9]+";
chr1\tmm9_refFlat\texon\t4822392\t4822462\t\.\t\+\t\.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "[0-9]+";
chr1\tmm9_refFlat\texon\t4827082\t4827155\t\.\t\+\t\.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "[0-9]+";
chr1\tmm9_refFlat\texon\t4829468\t4829569\t\.\t\+\t\.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "[0-9]+";
chr1\tmm9_refFlat\texon\t4831037\t4831213\t\.\t\+\t\.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "[0-9]+";
chr1\tmm9_refFlat\texon\t4835044\t4836816\t\.\t\+\t\.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "[0-9]+";
chr1\tmm9_refFlat\texon\t4847775\t4848057\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+";
chr1\tmm9_refFlat\texon\t4847775\t4848057\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1_dup1"; exon_number "[0-9]+";
chr1\tmm9_refFlat\texon\t4857551\t4857613\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+";
chr1\tmm9_refFlat\texon\t4857551\t4857613\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1_dup1"; exon_number "[0-9]+";
chr1\tmm9_refFlat\texon\t4868108\t4868213\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+";
chr1\tmm9_refFlat\texon\t4876825\t4876912\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+";
chr1\tmm9_refFlat\texon\t4879538\t4879683\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+";
chr1\tmm9_refFlat\texon\t4880821\t4880877\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+";
chr1\tmm9_refFlat\texon\t4881996\t4882150\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+";
chr1\tmm9_refFlat\texon\t4883498\t4883644\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+";
chr1\tmm9_refFlat\texon\t4885015\t4885086\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+";
chr1\tmm9_refFlat\texon\t4886437\t4887987\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+";
chr1\tmm9_refFlat\ttranscript\t4334224\t4350473\t\.\t-\t\.\tgene_id "Rp1"; transcript_id "Rp1"; ref_gene_id "Rp1";
chr1\tmm9_refFlat\ttranscript\t4481009\t4486494\t\.\t-\t\.\tgene_id "Sox17"; transcript_id "Sox17"; ref_gene_id "Sox17";
chr1\tmm9_refFlat\ttranscript\t4763279\t4775807\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15"; ref_gene_id "Mrpl15";
chr1\tmm9_refFlat\ttranscript\t4763279\t4775807\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; ref_gene_id "Mrpl15";
chr1\tmm9_refFlat\ttranscript\t4763279\t4775807\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; ref_gene_id "Mrpl15";
chr1\tmm9_refFlat\ttranscript\t4797974\t4836816\t\.\t\+\t\.\tgene_id "Lypla1"; transcript_id "Lypla1"; ref_gene_id "Lypla1";
chr1\tmm9_refFlat\ttranscript\t4847775\t4857613\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1_dup1"; ref_gene_id "Tcea1";
chr1\tmm9_refFlat\ttranscript\t4847775\t4887987\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1"; ref_gene_id "Tcea1";