Update Usage.md

WGLab · Jan 28, 2021 · ef52ea7 · ef52ea7
1 parent 431c428
commit ef52ea7
Showing 1 changed file with 5 additions and 11 deletions.
diff --git a/doc/Usage.md b/doc/Usage.md
@@ -15,7 +15,7 @@ liqa -task <task>:
 ## Step 1: Transforming isoforms to compatible matrix based on reference annotation file
 LIQA accepts two formats of reference annotation file. User can download the example reference file and data from the [example folder](https://github.com/WGLab/LIQA/tree/master/example):
 ### GTF format
-For example:
+For example `example.gtf`:
 ```
 chr21   HAVANA  gene    25639258        25717562        .       +       .       gene_id "ENSG00000154721.15"; gene_type "protein_coding"; gene_name "JAM2"; level 2; hgnc_id "HGNC:14686"; tag "overlapping_locus"; havana_gene "OTTHUMG00000
 078441.4";
@@ -30,17 +30,11 @@ ame "JAM2-206"; exon_number 1; exon_id "ENSE00003843052.1"; level 2; protein_id
 911.1"; havana_gene "OTTHUMG00000078441.4"; havana_transcript "OTTHUMT00000171347.2";
 ```
 ### UCSC all fields
-For example:
+For example `example.ucsc`:
 ```
-749     NM_001397       chr1    -       21543739        21616982        21546447        21616907        19      21543739,21548239,21551742,21553651,21554423,21560050,21562342,21563238,21564626,21571481,21573713,21582439,21584017,21585185
-,21586763,21599191,21605683,21616562,21616856,  21546624,21548335,21551933,21553719,21554534,21560154,21562420,21563337,21564737,21571596,21573856,21582631,21584083,21585332,21586885,21599404,21605825,21616649,21616982,     0       ECE1cmpl     cmpl    0,0,1,2,2,0,0,0,0,2,0,0,0,0,1,1,0,0,0,
-93      NM_001113348    chr1    -       21543739        21672034        21546447        21671871        19      21543739,21548239,21551742,21553651,21554423,21560050,21562342,21563238,21564626,21571481,21573713,21582439,21584017,21585185
-,21586763,21599191,21605683,21616562,21671868,  21546624,21548335,21551933,21553719,21554534,21560154,21562420,21563337,21564737,21571596,21573856,21582631,21584083,21585332,21586885,21599404,21605825,21616649,21672034,     0       ECE1cmpl     cmpl    0,0,1,2,2,0,0,0,0,2,0,0,0,0,1,1,0,0,0,
-749     NM_001113349    chr1    -       21543739        21616766        21546447        21616691        18      21543739,21548239,21551742,21553651,21554423,21560050,21562342,21563238,21564626,21571481,21573713,21582439,21584017,21585185
-,21586763,21599191,21605683,21616562,   21546624,21548335,21551933,21553719,21554534,21560154,21562420,21563337,21564737,21571596,21573856,21582631,21584083,21585332,21586885,21599404,21605825,21616766,      0       ECE1    cmpl    cmpl0,0,1,2,2,0,0,0,0,2,0,0,0,0,1,1,0,0,
-749     NM_001113347    chr1    -       21543739        21606183        21546447        21605927        17      21543739,21548239,21551742,21553651,21554423,21560050,21562342,21563238,21564626,21571481,21573713,21582439,21584017,21585185
-,21586763,21599191,21605683,    21546624,21548335,21551933,21553719,21554534,21560154,21562420,21563337,21564737,21571596,21573856,21582631,21584083,21585332,21586885,21599404,21606183,       0       ECE1    cmpl    cmpl    0,0,1,2,2,0,0
-,0,0,2,0,0,0,0,1,1,0,
+947     ENST00000397748.5       chr21   -       47556175        47575481        47556367        47575437        15      47556175,47556828,47557152,47558421,47558793,47565330,47565731,47566179,47570032,47570301,47571471,47571805,47572820,47574062,47575383,      47556408,47556967,47557248,47558560,47558837,47565492,47565861,47566241,47570164,47570439,47571651,47571894,47572949,47574246,47575481, 0       FTCD    cmpl    cmpl    1,0,0,2,0,0,2,0,0,0,0,1,1,0,0,
+947     ENST00000397743.1       chr21   -       47556692        47575481        47557159        47575437        13      47556692,47557152,47558421,47565330,47565731,47566179,47570032,47570301,47571471,47571805,47572820,47574062,47575383,47556987,47557248,47558560,47565492,47565861,47566241,47570164,47570439,47571651,47571894,47572949,47574246,47575481,   0       FTCD    cmpl    cmpl    -1,1,0,0,2,0,0,0,0,1,1,0,0,
+947     ENST00000397746.7       chr21   -       47556692        47575481        47556900        47575437        14      47556692,47557152,47558421,47558793,47565330,47565731,47566179,47570032,47570301,47571471,47571805,47572820,47574062,47575383,       47556987,47557248,47558560,47558837,47565492,47565861,47566241,47570164,47570439,47571651,47571894,47572949,47574246,47575481,  0       FTCD    cmpl    cmpl    0,0,2,0,0,2,0,0,0,0,1,1,0,0,
 ```
 This reference file can be downloaded at [UCSC](https://genome.ucsc.edu/cgi-bin/hgTables?command=start) by selecting "all fields from selected table" in output format.